Unmanned helicopter is undertaking more and more important combat missions, and deck motion is an important factor affecting the safety of its autonomous landing, thus the accurate estimation and compensation of deck motion becomes an urgent problem. To solve the problem, a method of deck motion estimation and compensation based on adaptive AR model and optimal preview control is proposed. When designing the deck motion estimator based on AR model, the time-variant factor is introduced to design the updating law of the adaptive model parameters, so as to optimize model performance. Simulation results show that the proposed method improves the accuracy of deck motion estimation to a certain extent, and its computation process is relatively simple. Then, the prediction signals generated by the deck motion estimator are introduced into the preview controller as the foreseeable future information, and the deck motion of the landing point is compensated based on the optimal control theory. This method solves the problem of phase delay of deck motion compensation system effectively and improves the deck motion tracking accuracy to a certain extent, so that it can increase the success rate of unmanned helicopter autonomous landing.