The ultra-high-speed aerodynamically alleviated marine vehicle (AAMV) is an unmanned surface vehicle (USV) with the advantages of fast speed, shallow draft, strong wind and wave resistance and long voyage, which fills the gap between high-speed aircrafts and low-speed surface vehicles. To explore the influence of waves on the motion characteristics of the ultra-highspeed AAMV, numerical research on stability of the ultra-high-speed AAMV at different speed and different sea states is carried out. The stability mathematical model of the ultra-high-speed AAMV is established based on the small disturbance linearization theory, and the stability of the vehicle is divided into longitudinal stability and lateral stability. Numerical results show that the ultra-high-speed AAMV shows good longitudinal and lateral stability at cruise speed. At the cruising phase, the pitch angle response, the roll angle response, and the heave response under sea state 5 are 0.210°, 0.0229° and 0.0734m, respectively. With the increase of speed, the aerodynamic force of the ultra-high-speed AAMV gradually increases, and the effect of aerodynamic alleviation is also enhanced accordingly, which greatly weakens the influence of waves on motions. The effect of aerodynamic alleviation can effectively improve the stability of the ultra-high-speed AAMV in waves.