Due to direct drive load of permanent magnet linear synchronous motor, various disturbances such as sudden load changes, friction and thrust fluctuations will also act directly on the motor mover without buffering. If not considered, the accuracy of the servo system will be seriously affected. In order to solve the adverse impact of the uncertain disturbance on the position servo system of the permanent magnet linear synchronous motor, the paper proposes a kind of robust backstepping control strategy. Firstly, the load force, thrust fluctuation and friction force are taken as total disturbance after analyzing the mathematic model of the permanent magnet linear synchronous motor. Then, the paper designs a kind of observer to estimate the total disturbance. The estimated value is introduced into the backstepping controller as a role of compensation of the disturbance. The paper also uses Lyapunov function to analyze the stability of the system. Finally, compared with the backstepping control without disturbance compensation, the simulation results show that the proposed control strategy can effectively eliminate the adverse effects, enhance the robustness of the servo system and improve the position tracking accuracy of the motor.