In order to establish a sparse and accurate ship motion prediction model, a novel Bayesian probability prediction model based on relevance vector machine (RVM) was proposed for nonparametric modeling. The sparsity, effectiveness, and generalization of RVM were verified from two aspects: (1) the processed Sinc function dataset, and (2) the tank test dataset of the KRISO container ship (KCS) model. The KCS was taken as the main research plant, and the motion prediction models of KCS were obtained. The ε-support vector regression and υ-support vector regression were taken as the compared algorithms. The sparsity, effectiveness, and generalization of the three algorithms were analyzed. According to the trained prediction models of the three algorithms, the number of relevance vectors was compared with the number of support vectors. From the prediction results of the Sinc function and tank test datasets, the highest percentage of relevance vectors in the trained sample was below 17%. The final prediction results indicated that the proposed nonparametric models had good prediction performance. They could ensure good sparsity while ensuring high prediction accuracy. Compared with the SVR, the prediction accuracy can be improved by more than 14.04%, and the time consumption was also relatively lower. A training model with good sparsity can reduce prediction time. This is essential for the online prediction of ship motion.