This paper proposes a method for the online parameter identification of nonlinear ship motion systems. First, the motion system of a ship is nonlinear, and in the course of sailing, the motion parameters of the ship will change with the change of the motion state of the ship and the sailing environment. To achieve the effect of real-time identification, we adopted an online receding horizon identification method. Second, identification parameters are the essential elements in the navigation control of intelligent merchant ships, and high-precision identification results can achieve better control effects. Therefore, we used an unscented Kalman filter (UKF) that has simpler mathematical structure and higher feedback efficiency than other identification algorithms listed in this paper, such as extended the Kalman filter, Kalman filtering and Ordinary Least Squares, as the identification scheme design algorithm, which is applied to ship motion system identification. Then, to solve the problem of significant identification errors in complex environments, we design a navigation identification framework combining a UKF and rolling wavelet denoising to realize the effect of the online identification of ships. Finally, a Korea Research Institute of Ships and Ocean Engineering (KRISO) Container Ship (KCS) was used for a self-navigation model experiment and data collection. The collected data and identification data were compared and analyzed. By comparing different identification algorithms before and after denoising, it was verified that the UKF algorithm proposed in this paper is superior relative to other traditional algorithms in identifying ship motion systems.