To obtain more effective prediction effects,based on study of LMS algorithm,affine projection algorithm is proposed in this paper which is apply to estimating AR model parameters.The adaptive AR predicted model is built by using measured dynamic data combining with AIC criterion and the model is applied in the ship motion prediction.After comparative analysis of the simulation results,the predicted model based on Affine projection algorithm can get more precise prediction and the prediction time is more longer.The convergence rate of adaptive estimation of parameters about AR model is faster compared with LMS algorithm,LMS-Newton algorithm and NLMS algorithm.So the method provides theoretical basis for real time on-line prediction of ship motion.