After he retired Ma Lin would take up coaching where he started off with
Dalian Yiteng as an assistant before joining Liaoning once more as one of their assistants. After the team's head coach
Dimitar Penev left during the 2003 league season Ma Lin would go on to be promoted as the team's manager where he would lead them to a mid-table sixth-place finish. He would then be given a full season to manage the squad and go on to lead the team to an improved fourth-place finish, however despite this improvement Ma Lin was allowed to leave and was replaced by the experienced coach
Wang Hongli. He would take over the management position at
Chongqing Lifan at the beginning of the 2005 league season where he was unable to improve the team's fortunes as a lowly club within the top tier and left after one season. He would then take the management position at second tier side
Jiangsu Sainty where he unable to aid them in their promotion push and resigned during the league season. After a short period outside management Ma Lin returned to Liaoning after
Werner Lorant was sacked and was brought in to help the team in their relegation battle during the 2008 league season. Unable to achieve this the club stuck with Ma Lin and he immediately repaid their loyalty by winning the division title and re-promotion back to the top tier after only one season. On 26 November 2017 Ma Lin was appointed the new manager at
Dalian Yifang. On 20 March 2018, he was relieved of duty as manager of Dalian Yifang and replaced by
Bernd Schuster. ==Career statistics==