Controllable pitch propeller is widely used in ship thrust system for its good property. In this paper, we propose a joint controller with load protection for controllable pitch propeller. Based on an in-depth study of the thrust unit and its control system of the controllable pitch propeller, the models of the speed and pitch control subsystems are built and tuned with good closed-loop characteristics. According to the energy conversion and balance condition between the ship, propeller and diesel engine, an optimal matching control algorithm of engine speed and pitch with load protection is developed for the combined control mode. Take the highest thrust effectiveness as the optimization goal, the optimization mathematical model with constraints is established and solved using exterior penalty and standard Particle Swarm Optimization (SPSO). The effectiveness and superiority of the proposed control algorithm for combined control mode is verified by comparing with the speed control mode which is common used by ships.