Hugues was a son of Jean "the old" of Chalon (1190–1267), Sire of Salins and his third wife Laura of Commercy (d. 1275), sister of Simon IV, Count of Saarbrücken.
Hugues could not prevent military action from both sides and the war continued for decades.
In 1300 he defended himself before the Roman curia in Rome against charges from the cathedral chapter and others, that he had defrauded his brother John I of Chalon-Auxerre and that he had sold off ecclesiastical possessions for benefits and allegiances.
Pope Boniface VIII removed him from his bishopric at Liège and instead made him Archbishop of Besançon.
Hugues participated in the Council of Vienne (1311–1312) convoked by Pope Clement V, where he contracted an illness and died, probably around 22 February 1312.