Thauvin was injured during Marseille's 3-1 victory at Guingamp on April 20 and exacerbated the problem in training, although he recovered in time to help his side finish the 2018-19 season with back-to-back victories as they claimed fifth place in Ligue 1.
However, the issue continued to hamper the France international, who has played just 10 minutes as a substitute in the top flight this term, and he has made the decision to go under the knife in order to return to full fitness.
A statement on the club's official website said: "Florian Thauvin suffered an accidental ankle injury in a match about four and a half months ago.
🔵 Medical Announcement: @FlorianThauvin and the Club have agreed for the player to undergo an operation in the coming days. He will undergo a period of unavailability until the winter break. pic.twitter.com/EGea61pV1J— Olympique Marseille (@OM_English) September 11, 2019
"This type of lesion, small, very localised, usually allows [the player] to resume after appropriate care and rest. His current progress has allowed him to return to the group but the player still feels a discomfort.
"In order to be able to return to 100 per cent of his capacity, Florian and Olympique de Marseille have decided to carry out a small operation (arthroscopy) in the coming days.
"His period of unavailability should last until the winter break."
The news means Thauvin is likely to be out of action until January, with Ligue 1's mid-season break scheduled to run from December 20 until January 10.
Thauvin's injury problems hampered his side's progress last season, with a heel injury in October 2018 forcing him to miss a Europa League defeat to Lazio before his April absence left Marseille short of creativity at a key stage in the season.
Andre Villas-Boas' side had a mixed start to the new campaign, recovering from an opening-day defeat at home to Reims to go unbeaten in their past three league matches.
Marseille travel to Stade Louis II to face Monaco in Ligue 1 on Sunday.