The aim of this paper is to propose a novel method for identifying the hydrodynamic parameters of a deep‐sea mining vehicle during deployment and retrieval. The proposed approach combines numerical simulation with a nonlinear filter. Initially, a dedicated hydrodynamic model for the deployment and retrieval of the mining vehicle is constructed. The identification process commences with simulations based on computational fluid dynamics (CFD). This approach utilizes CFD to simulate the motion of the deep‐sea mining vehicle during deployment and retrieval, employing an implicit solution approach to analyze its motion in Heave and Yaw degrees of freedom under periodic external forces. Consequently, this provides hydrodynamic performance data. Subsequently, the unscented Kalman filter (UKF) estimator is applied to optimally solve an augmented matrix that incorporates both motion data and hydrodynamic parameters, yielding numerical values for the hydrodynamic parameters. Simulation results demonstrate that, in comparison to motion performance obtained by the CFD method, the hydrodynamic model derived from UKF enables an effective prediction of the motion of the deep‐sea mining vehicle, with prediction errors consistently below 6%.