As an important interface between unmanned aerial vehicles (UAVs) and ships, the stability and motion control compensation technology of the shipborne UAV landing platform are paramount for successful UAV landings. This paper has designed a new control compensation method for an autonomous UAV landing platform to address the impact of complex sea conditions on the stability of UAV landing platforms. Firstly, the parallel Stewart platform was introduced as the landing platform, and its structure was analyzed with forward and inverse kinematic calculations conducted in Matlab to verify its accuracy. Secondly, a least-squares recursive AR prediction algorithm was designed to predict the future attitudes of ships under varying sea conditions. Finally, the prediction algorithm was combined with the platform’s control strategy and a dual-sensor system was adopted to ensure the stability of the UAV landing process. The experimental results demonstrate that these innovative improvements enhanced the compensation accuracy by 59.6%, 60.3%, 48.4%, and 47.9% for the rolling angles of 5° and 10° and the pitching angles of 5° and 10°, respectively. Additionally, the compensation accuracy for the roll and pitch in sea states 2 and 5 improved by 51.2%, 59.4%, 58.7%, and 55.9%, respectively, providing technical support for UAV missions such as maritime rescue and exploration.