The invention discloses a brake mechanism of a marine gearbox. The brake mechanism comprises a case body, a box body, an insertion rod and an electric pushing rod, wherein an insertion hole is formedin one side of the case body; the inner part of the insertion hole is rotatably connected with a rotary shaft; one end of the rotary shaft is fixedly connected with a gear; the peripheral outer side of one end, away from the gear, of the rotary shaft is fixedly connected with a first magnet; a tube body is connected on the peripheral outer part of the rotary shaft in a sleeving mode; and the tubebody is rotatably connected to one side of the case body through a first bearing. In a using process, an electric pushing rod switch controls the electric pushing rod to extend while brake effect needs to achieve for the rotary shaft, so that a friction block is in contact with a friction pad, a fixed circular disc stops rotation, the brake effect for the rotary shaft is achieved as a second magnet inside the tube body applies repulsive force to the first magnet in a moving process, and the friction block is not in direct contact with the rotary shaft, and therefore, abrasion on the rotary shaft is reduced, replacing times of the rotary shaft are reduced, and labour intensity of a worker is reduced.