This paper proposed a method of online non-parameter identification of nonlinear ship motion systems. Firstly, we use Mariner to generate a certain amount of ship motion data to train the LWPR model. Then the ship travels along a set track. During this process, the sensors continuously obtain the distance, radial velocity and azimuth of the ship relative to the ship, and then completes the construction of simulation data. Next, the performance of the algorithm is verified which uses the Kalman filtering framework. Finally, the estimated value is further used for updating the LWPR model to achieve the purpose of online learning, and the updated model will be used for the next prediction. The experimental results show that the online modeling and tracking method proposed in this paper has higher tracking accuracy than the parameter estimation techniques.