A predictive functional control method based on disturbance observer is proposed to improve the performance of the permanent magnet linear synchronous motor servo system, which is usually characterized by nonlinearity, uncertainty and disturbance. The disturbance observer is applied to estimate the disturbance in real time and then compensation current is produced to restrain the load disturbance in the speed controller. The simulation results show that the controller based on the disturbance observer and predictive functional controller can improve the response speed and steady-state accuracy of the system. As the controller shows strong robustness and anti-disturbance, it can be used to effectively control the complex systems.