After his retirement as a player, Mori managed the Seibu Lions from 1986–1994, leading the team to 6 of the 8 Japan Series championships of the Invincible Seibu dynasty. He won the Matsutaro Shoriki Award in 1986 and 1990. Mori managed the Yokohama BayStars in 2001–2002.
Mori participated in 27 of the 73 Japan Series contested, as a player, coach, and manager, as of 2023, with him winning 21 of the 27, making him the most decorated individual in NPB history.