Born in Cromarty, he was educated in a parish school where he reportedly showed a love of reading. At 17 he was apprenticed to a stonemason, and his work in quarries, together with walks along the local shoreline, led him to the study of geology. In 1829 he published a volume of poems, and soon afterwards became involved in political and religious controversies, first connected to the Reform Bill, and then with the division in the Church of Scotland which led to the Disruption of 1843.
In 1834 he became accountant in one of the local banks, and in the next year brought out his Scenes and Legends in the North of Scotland. In 1840 the popular party in the Church, with which he had been associated, started a newspaper, The Witness, and Miller was called to be editor in Edinburgh, a position which he retained till the end of his life.
Among his geological works are:
Other books are:
Of the geological books, perhaps The Old Red Sandstone was the best-known. The Old Red Sandstone is still an expression used to describe sedimentary rock deposited after the Acadian Orogeny in the late Silurian, and before the Carboniferous Period.
Though Miller's strong religious sense led him to oppose bitterly the emerging theories of evolution, he was also a firm believer in the antiquity of the Earth and of Noah's flood not having been global in extent. .
For most of the year 1856, the brilliant researcher and speaker had been bothered by terrible headaches that seemed to burn inside his head. Had he lived in the 20th century, Miller's doctors could have diagnosed the problem. Perhaps it was a tumor that caused the headaches, and later, the awful hallucinations. Victorian-era medicine could not help. He feared that he might harm his wife or children during his delusions in which he pursued imaginary robbers with his gun. Miller committed suicide the night he finished checking printers' proofs for his book on Scottish fossil plants and vertebrates, The Testimony of the Rocks. Before his death, he wrote a poem called Strange but True
A shocked Western world mourned him, and his funeral procession was among the largest in the memory of Edinburgh residents.
Miller's death was very tragic, and his life brief, but he left a heritage of new discoveries of several Silurian sea scorpions (the eurypterid genus Hughmilleria was named in his honor), and many Devonian fishes, including several placoderms (the arthrodire Millerosteus also honored him), intriguingly described in his popular books. Though he had no academic credentials, he is today considered one of Scotland's premier paleontologists.
His home in Cromarty is open as a geological museum, with specimens collected in the immediate area; a week-end event at the site in 2008 was part of celebrations marking the bicentenary of the Geological Society of London.Miller was mentioned in the song "Idea Track" by Scottish band Idlewild.