Wehler is one of the most famous members of the so-called Bielefeld School, a group of historians who used the methods of the social sciences to analyze history. Wehler's speciality is the Second Reich. He was one of the more famous proponents of the Sonderweg (Special Path) thesis that argues Germany in the 19th century had only a partial modernization. Wehler has argued that Germany was the only nation to be created in Western Europe through a military "revolution from above", which happened to occur at the same time that the agricultural revolution was fading while the Industrial Revolution was beginning in Central Europe. As a result, the economic sphere was modernized and the social sphere partially modernized. Politically, in Wehler's opinion the unified Germany retained values that were aristocratic and feudal, anti-democratic and pre-modern. In Wehler's view, it was the efforts of the reactionary German élite to retain power that led to the outbreak of the First World War in 1914, the failure of the Weimar Republic and the coming of the Third Reich. Wehler has asserted that the effects of the traditional power elite to maintain power up to 1945 "and in many respects even beyond that" took the form of "a penchant for authoritarian politics; a hostility toward democracy in the educational and party system; the influence of preindustrial leadership groups, values and ideas; the tenacity of the German state ideology; the myth of the bureaucracy; the superimposition of caste tendencies and class distinctions; and the manipulation of political antisemitism". Wehler has in particular been critical of what calls Otto von Bismarck's strategy of “negative integration” in which Bismarck sought to create a sense of Deutschtum (Germanism) and consolidate his power by subjecting various minority groups such as Roman Catholics, Alsatians, Poles, and Social Democrats to discriminatory laws. Wehler is one of the foremost advocates of the “Berlin War Party” historical school, which assigns the sole and exclusive responsibility for World War I to the German government.
Wehler has argued that the aggressive foreign policies of the German Empire, especially under Kaiser Wilhelm II, were largely part of an effort on the part of the government to distract the German people from the lack of democracy in their country. This Primat der Innenpolitik ("primacy of domestic politics") argument to explain foreign policy, for which Wehler owes much to the work of Eckart Kehr, puts him against the traditional Primat der Außenpolitik ("primacy of foreign politics") thesis championed by historians such as Gerhard Ritter, Klaus Hildebrand, Andreas Hillgruber, and Ludwig Dehio. In the 1970s, Wehler was involved in a somewhat discordant and acrimonious debate with Hildebrand and Hillgruber over the merits of the two approaches to diplomatic history. Hillgruber and Hildebrand argued for the traditional Primat der Aussenpolitik approach with empirical research on the foreign-policy making elite while Wehler argued for the Primat der Innenpolitik approach by treating diplomatic history as a sub-branch of social history with the focus on theoretical research. The two major intellectual influences Wehler cites are Karl Marx and Max Weber.
Wehler has often criticized traditional German historiography with its emphasis on political events, the role of the individual in history and history as an art as unacceptably conservative and incapable of properly explaining the past. In a 1980 article, Wehler mocked those who sought to explain Nazi Germany as due to some defect in Adolf Hitler's personality by commenting: "Does our understanding of National Socialist policies really depend on whether Hitler had only one testicle?...Perhaps the Führer had three, which made things difficult for him-who knows?...Even if Hitler could be regarded irrefutably as a sado-masochist, which scientific interest does that further?...Does the "Final Solution of the Jewish Question" thus become more easily understandable or the "twisted road to Auschwitz" become the one-way street of a psychopath in power?". Wehler sees history as a social science and contends that social developments are frequently more important than politics. In his view, history is a "critical social science" that must examine both the "temporal structures" of a society and encourage a "freer critical awareness of society". Wehler has advocated an approach he calls Historische Sozialwissenschaft (Historical Social Science), which favors integrating elements of history, sociology, economics and anthropology to study in a holistic fashion long-term social changes in a society. In Wehler's view, Germany between 1871–1945 was dominated by a social structure which retarded modernization in some areas while allowing it in others. For Wehler, Germany's defeat in 1945 finally smashed the "pre-modern" social structure and let Germany become a normal 'Western' country.
Wehler is a leading critic of what he sees as efforts on the part of conservative historians to whitewash the German past). He played an important part in the Historikerstreit (historians' dispute) of the 1980s. The debate began after the publishing of an article by the philosopher Ernst Nolte in the German newspaper Frankfurter Allgemeine Zeitung on June 6th of 1986. In his article, Nolte claims that there was a connection by cause between the Gulag and the Nazi extermination camps, the previous supposedly having effected the latter, which he called an overshooting reaction ("überschießende Reaktion"). This infuriated many (and mainly left wing) intellectuals, among them Wehler and the philosopher Jürgen Habermas. They strongly rejected Nolte's thesis and presented a case for seeing the crimes of Nazi Germany as uniquely evil (something which in the view of Nolte's defenders, Nolte never disputed in the first place). Wehler was ferocious in his criticism of Nolte and wrote several articles and books that by Wehler’s own admission were polemical attacks on Nolte. In his 1988 book about the Historikerstreit entitled Entsorgung der deutschen Vergangenheit?: ein polemischer Essay zum "Historikerstreit" (Exoneration of the German Past?: A Polemical Essay about the 'Historikerstreit'), in which Wehler criticized every aspect of Nolte's views, and in which Wehler called the Historikerstreit a "political struggle" for the historical understanding of the German past between "a cartel devoted to repressing and excusing" the memory of the Nazi years, of which Nolte was the chief member, against "the representatives of a liberal-democratic politics, of an enlightened, self-critical position, of a rationality which is critical of ideology". In the same book, and speaking not only of the work of Nolte, but also of the work of Klaus Hildebrand, Andreas Hillgruber, Joachim Fest and Michael Stürmer, Wehler wrote: "This survey is directed-among other matters-against the apologetic effect of the tendency of interpretations that once more blame Hitler alone for the 'Holocaust'-thereby exonerating the older power elites and the Army, the executive bureaucracy, and the judiciary ...and the silent majority who knew". Speaking of the political importance of the Historikerstreit, Wehler described the debate as "The Historikerstreit is, in sum, more than a strictly scholarly controversy within scholarly limits".
Along somewhat similar lines, in September 1990 Wehler strongly condemned a newspaper opinion piece by Harold James which suggested national legends and myths were needed to sustain national identity. During the "Goldhagen Controversy" of 1996, Wehler was a leading critic of Daniel Goldhagen, especially in regards to the latter's claims about alleged German "eliminationist anti-Semitism", through Wehler was more sympatric towards Goldhagen's claims about the motives of Holocaust perpetrators.
Wehler's work has faced criticism. From the right, Otto Pflanze claimed that Wehler's use of such terms as "Bonapartism", "social imperialism" "negative integration" and Sammlungspolitik has gone beyond mere heuristic devices and instead become a form of historical fiction. The German conservative historian Thomas Nipperdey has argued that Wehler presented German elites as more united then they were, focused too much on forces from above and not enough on forces from below in German society, and presented a too stark contrast between the forces of order and stabilization vs. the forces of democracy with no explanation for the relative stability of the Empire. In Nipperdey's opinion, Wehler's work fails to explain how the Weimar Republic occurred. In a 1975 book review of Wehler's Das Deutsche Kaiserreich, Nipperdey concluded that a proper history of the Imperial period could only be written by placing German history in a comparative European and trans-Atlantic perspective, which might allow for "our fixation on the struggle with our grand-grandfathers" to end. From the left, Wehler has been criticized by two British Marxist historians, David Blackbourn and Geoff Eley who rejected the entire concept of the Sonderweg as a flawed construct supported by a "a curious mixture of idealistic analysis and vulgar materialism" that led to an "exaggerated linear continuity between the nineteenth century and the 1930s". In the view of Blackbourn and Eley, there was no Sonderweg, and it is ahistorical to judge why Germany did not become Britain. Moreover, Eley and Blackbourn argued that after 1890 there was a tendency towards greater democratization in German society with the growth of civil society as reflected in the growth of trade unions and a more or less free press.
In 2000, Wehler became the eighth German historian to be inducted as an honorary member of the American Historical Association. Wehler accepted this honor with some reluctance as previous German historians so honored have included Leopold von Ranke, Gerhard Ritter and Friedrich Meinecke, none of whom Wehler considers to be proper historians.
In a 2006 interview, Wehler supported imprisonment of David Irving for Holocaust Denial under the grounds that “The denial of such an unimaginable murder of millions, one third of whom were children under the age of 14, cannot simply be accepted as something protected by the freedom of speech”. In recent years, Wehler has been a leading critic of Turkey's possible adhension to the European Union.