After retirement, in November 1980, Mori became an assistant coach for the Japan national team under new manager Saburo Kawabuchi. Mori was promoted to manager in April 1981. He managed at 1982 Asian Games and 1984 Summer Olympics qualification. At 1986 World Cup qualification in 1985, Japan defeated Singapore, North Korea and Hong Kong to reach the final round of the East Asian zone to play South Korea. Japan lost 1-3 on aggregate. Mori then led the team to the 1986 Asian Games in Seoul and resigned following the team's failure to reach the second round. In 1992, Mori became a manager for Urawa Reds. However, Urawa Reds finished at the bottom place in 1993 season and he resigned end of the season. In 1998, he signed with Avispa Fukuoka and he managed the club in 1 season.