Deep-sea mining is the advanced deepwater and ultra-deepwater mining technology with high difficulty. In previous studies, the analysis of the coupling of the dynamic positioning process with the riser and equipment was insufficient. The hydrodynamic performance of the mining vessel is analyzed by the potential flow theory, and the dynamic modeling of the riser and the relay cabin is established by the lumped mass method and Morison equations. The PID controller with Kalman filtering is employed to model the ship dynamic positioning system and simulate the thrust allocation unit, fully considering the influence of the dynamic positioning on the coupled motion system. The time-domain coupling numerical analysis of the deep-sea mining system during the dynamic positioning of the mining vessel is carried out to obtain the movement of the mining vessel and relay cabin under specified sea state, the riser tension and the propeller thrust. The influence of the dynamic positioning system is the also analyzed. The simulation can provide reference for the design and analysis of the deep-sea mining.