Linois joined the French Navy in 1776, serving in the English Channel and Spanish waters, followed by voyages to Ile de France (Mauritius) and Réunion and the French West Indies. He was promoted to lieutenant in 1789 before being posted to the Indian Ocean. After his return to France in 1794, he was based in Brest. Linois was captured by the Royal Navy while his ship was protecting a convoy of wheat from the United States. He was exchanged and promoted to captain. The following year he was captured again at the battle of Groix and again exchanged. In 1796 he was part of the unsuccessful expedition to invade Ireland.
In 1799 he was promoted to Rear-Admiral (contre-amiral) and sent to the Mediterranean under Admiral Bruix. As second in command of the squadron under Admiral Ganteaume, he attacked Elba in 1801. Then in command of a small squadron based in Cadiz, he fought a larger British squadron under Sir James Saumarez in the Battle of Algeciras. His squadron prevailed during the first part of the battle, capturing HMS Hannibal, but on the return to Cadiz, two Spanish ships who had joined him were fooled into firing on each other by a British night attack and were lost.
In 1803 Napoleon Bonaparte appointed him to command the French forces in the Indian Ocean and, flying his flag aboard the 74-gun-ship Marengo, he harried British merchant ships across the ocean and into the China Seas. One embarrassing incident was the Battle of Pulo Aura in 1804 when a squadron of French naval ships commanded by Linois encountered the British China Fleet which consisted of lightly armed merchant ships. The British ships outnumbered Linois and they manoeuvred as though would fight to defend themselves and some of the ships flew naval ensigns. Linois was persuaded that the fleet was defended by a number of naval escorts and so he retired instead of attacking the virtually defenceless fleet.
However, on his return to France he ran into a large British squadron under Admiral Warren off Cape Verde. He was wounded and captured again but this time as Napoleon had stopped the practice of exchanging officers he was held until Napoleon fell in 1814. He was appointed comte de Linois in 1810 by Napoleon.
Following the Bourbon restoration, Louis XVIII named him to be Governor of Guadeloupe but as Linois supported Napoleon during the Hundred Days he was forced to resign after the battle of Waterloo. He was court martialled but acquitted in 1816. However, he was placed in retirement and never served again, although he was appointed as an honorary Vice-Admiral (vice-amiral) in 1825. He lived in Versailles and died in 1848.
Linois is a minor recurring character in the Aubrey–Maturin series by Patrick O'Brian, where he is, incidentally, represented as an older man than he actually was as the time (Aubrey describes him as 'a deep old file' in HMS Surprise). The Battle of Pulo Aura is also described in Newton Forster, or The Merchant Service, written in 1832 by Frederick Marryat.