Decoux was born in Bordeaux, one of three children of a family originally from Upper Savoy. In 1901, aged about 16, he entered the École navale. He was promoted to aspirant second class in 1903, to aspirant first class the following year, ship-of-the-line ensign (sub-lieutenant) in 1906, ship-of-the-line lieutenant (lieutenant) in 1913, corvette captain (lieutenant-commander) in 1920, frigate captain (commander) in 1923, ship-of-the-line captain in 1929 and rear admiral (one-star rear admiral) in 1935. He was appointed commander of the defence sector at Toulon in 1938 and promoted to vice-admiral (two-star rear admiral).
On 13 January 1939, Decoux was appointed Commander-in-Chief of the Naval Forces in the Far East by President Albert Lebrun. He assumed his new appointment, with the rank of squadron vice-admiral (vice admiral), on 12 May.
Like his predecessor, Decoux initially wished to continue the fight against the Axis powers, but he swore allegiance to Pétain's regime after realizing that his meager armed forces were no match for the Japanese.
Decoux reportedly received demands from the Japanese in early August for permission to move troops through Tonkin (later Vietnam) in order to build air bases and block Allied supply routes to China. Decoux cabled his Vichy superiors for aid, but when no help was forthcoming signed a treaty on 20 September 1940 opening Haiphong harbor to the Japanese and giving them the right to station troops in the region.
Decoux worked to improve relations between French colonists and the Vietnamese. He established a grand federal council containing twice as many Vietnamese members as Frenchmen and installed Vietnamese in civil-service positions with equal pay to that of French officials. The Indochinese Federal Council, which was composed only of Indochinese, and later the Grand Federal Council, were the formal structures that Decoux felt he needed to build to develop the Indochinese federal consciousness simultaneously with the elevation of the elite. Rather than a legislative or executive body, the Federal Council in both its forms was a body consisting of non-elected indigenous elites. These gave their opinions to the Governor General to assist him in his decision-making, and served as a forum to strengthen relations between these elites and the authorities. The GFC replaced the IFC in 1943 by introducing 23 French representatives (from the economy's principal sectors, making it, according to Decoux, more representative) and adding five local members, thereby ensuring that the Indochinese presence outnumbered the European. Decoux believed this would reverse the reluctance of the local population to accept the politics of collaboration. In addition he apparently wished to show goodwill toward the Indochinese peoples following Roosevelt's public statement that maintaining French sovereignty in Indochina was not a principal objective of the United States. The French colonial authorities learnt of this policy through BBC broadcasts.
One writer claims that Decoux remained unconcerned by the famine of 1945. During this time over one million Vietnamese died of starvation in the countryside and urban cities and the author asserts that the Decoux government did nothing to help the Vietnamese peasants, farmers, and poor, despite soliciting and courting the Vietnamese elite. However, archival records show that Allied bombardment of railways and the requisitioning of boats by the Japanese made it impossible to transport rice from Cochinchina to Tonkin.
Arrested and tried after the war, Decoux was not convicted. He was restored to his rank and prerogatives in 1949. He later wrote the book A la barre de l'Indochine. He died in Paris in 1963.