This paper proposes a new position controller for permanent magnet linear synchronous motor (PMLSM), which is robust against load disturbances, torque ripple and parameter variations. The controller, using a disturbance observer, is based on an acceleration control loop. According to the current and position information, the disturbance observer estimates the disturbance and parameter variations feedback to the inner current loop. Also the feedback controller and disturbance observer all adopt variable-structure controllers whose structure are changed continuously by fuzzy logic so that they suppress the observer noise. The effectiveness of the proposed controller is verified by experimental results. Disturbance suppression and improvement of phase delay are attained.