The invention provides a rudder protection method in a ship stopping state. When a ship stops, the ambient wind and waves pass through rudder blades to drive a rudder of a ship to rotate passively, when the rudder angle the rudder of the ship rotates reaches the position of the limit rudder angle, a limit switch sends a start signal to an electronic control box. The electronic control box receiving the start signal drives the ship's rudder to rotate actively, when the ship's rudder rotates to the position of 0-degree rudder angle, an induction switch sends a stop signal to the electronic control box, and the electronic control box receiving the stop signal makes the ship's rudder stop rotation through a control pump station. According to the method, the rudder is prevented from being damaged by impact of environmental wind and waves in the state of stopping, and energy consumption and labor can be saved.