After he retired Shandong offered him a position as the boss of media presentation, however due to his high-profile within China he was linked to numerous management positions. He would eventually go on to achieve the necessary coaching certificates required for a management position and he was expected to become an assistant within the
Chinese Football Association. On 8 August 2010 he would accept the position of interim head coach for the
Chinese women's team up to the
2010 Asian Games, which made him the youngest coach to ever manage the team. At the Games, Li would guide the team to the semi-finals where they lost 1–0 to
Japan. This would be good enough for Li to be offered an extension to his contract and guide the team through the
2012 Summer Olympics qualifiers. However, they failed to qualify and Li resigned. On 3 December 2021, Li was appointed as the new manager of the
Chinese national team, succeeding his 2002 World Cup teammate
Li Tie. He started his tenure disappointingly with two away losses: 2–0 to Japan and 3–1 to Vietnam. Li was dismissed in March 2022 after drawing 1 and losing 3 of his 4 games in charge. On 8 July 2024, Li was appointed general manager of Chinese Super League club
Cangzhou Mighty Lions. However, a mere days later on 16 July, he swapped positions with then-manager
Zhao Junzhe and began serving as the club's head coach with Zhao as the new general manager. On 18 January 2025, Li returned to fellow Chinese Super League club
Qingdao Hainiu (formerly named Qingda Janoon) as their new head coach, whom he had previously managed in 2014. Former Chinese international footballer
Hao Junmin also joined his coaching staff team. On 22 December 2025, the club annouanced Li's departure after the 2025 season. ==Honours==