Different kinds of underwater vehicles are widely used in oceanographic research, marine resource exploration and naval defense. Docking operation is an essential task that can facilitate better energy supply and information exchange for underwater vehicle. This paper proposes a novel docking method for underwater vehicle-manipulator system (UVMS) based on manipulator-aided operation, and modeling and dynamic simulation are implemented by multi-body technique. The manipulator mounted on the underwater vehicle is applied to grasp the assisted docking handle, and the connector positioned on the underwater vehicle is driven to the docking station point only through the motion of manipulator joints. In the docking process, the configuration of the UVMS transforms from a floating base multi-body system into a serial manipulator with a fixed end-effector. The kinematic and dynamic models of the underwater vehicle equipped with the underwater manipulator are developed. By planning the motion of the manipulator, the processes of approaching, grasping, and mating operation under manipulator-aided are simulated. The dynamic analysis of the whole docking process is given, and the simulation results suggest that the novel docking method has the advantages of high efficiency and strong environment adaptability.