The invention discloses a hydraulic control system of a full-rotation rudder propeller and a control method thereof. The hydraulic control system of the full-rotation rudder propeller comprises two balancing valves and two corresponding bypass damping holes, wherein two ends of each of the two bypass damping holes are correspondingly connected with a pilot control pressure channel of the corresponding balancing valve and a system overflow filling oil mouth. The control method comprises the steps that when the full-rotation rudder propeller rotates back, an outlet of one of the balance valves and the corresponding bypass damping hole will form a hydraulic half-bridge, high-pressure oil subjected to pressure dividing and filtering by the hydraulic half-bridge will act on the pilot control pressure channel of the other balancing valve to open the channel, and a back pressure is formed at the position of a working oil mouth of a hydraulic motor. According to the design, the system eliminates the phenomenon of vibration of full-rotation rudder paddle back rotation and improves operation comfort and reliability.