In this paper, the longitudinal control system for full-submerged hydrofoil based on wave prediction was proposed to exclude human operation and to improve the performance of contouring waves. The proposed control system consists of optimal preview servo system, Kalman filter and generation of future reference input and future wave disturbance. In the proposed control system, the wave disturbance and the wave elevation were filtered and predicted by using sensor signals, Kalman filter, 30th linear prediction model and the augmented system. Then the future reference input and the future wave disturbance were generated by using predicted wave disturbance and wave elevation, and were used to calculate the feedforward control input in the optimal preview servo system. And also the future reference was modified based on the significant wave height for ship height control. The simulation results show that the proposed control system has good performance of contouring waves in the follow sea and the hydrofoil regulates heave and pitch motion in low significant wave height and contours the waves in high significant wave height without human operation. And also the experiment was performed to confirm the algorithm of filtering of wave disturbance and hydrofoil motion, and calculation of wave elevation.