The invention discloses an anti-scale method and device of a filter used in a ship ballast water management system. The device comprises a coarse filter screen, a fine filter screen, a back-washing unit, a sewage discharge unit, and a control system; the coarse filter screen, a first partition plate, the fine filter screen, another partition plate, and the sewage discharge unit are horizontally arranged in the filter cavity; a control unit is part of main control equipment; the first partition plate between the fine filter screen and the coarse filter screen and the filter cavity form a filtering cavity, a water inlet is arranged on the filter shell, is above the coarse filter screen, and is communicated with the filter cavity; and a water outlet is arranged in the filter shell and is communicated with the filtering cavity. The device also comprises a variable-frequency processing unit, which is composed of a signal generator controlled by the control system and electromagnetic coils, and the electromagnetic coils are winded around the coarse filter screen. The provided anti-scale method and device solve the problem that conventional ship ballast water filter is easily obstructed during the application process, and the anti-scale device has the advantages of high integration level, small volume, and high intelligentization degree, and can meet the application requirements of a ship ballast water management system.