Based on Morison equation, a dynamics model of water-exit missile under wave disturbance was built, which takes the coupling between wave and motion of missile into account. The water-exit motion of small submarine-launched missile was simulated and analyzed. The effects of coupling between wave and motion of missile body to wave disturbance, illustrated by change process of attitude of missile, were studied. The influences of sea condition, wave phase, velocity and attitude of missile to the motion of water-exit course were analyzed. The result indicates that the characteristics of submarine-launched, which are small in size and fast in water-exit, reduce the impact of wave to attitude of missile. In addition, the wave disturbance to high-speed water-exit missile is significantly affected by sea condition, duration of water-exit course and wave phase. The dynamic model which takes the coupling between wave and motion of missile into account is more accurate.