This paper presents that our proposed docking system could apply for a new Remotely Operated Vehicle(ROV). The authors have proposed a 3D-perception based Move on Sensing (3D-MoS) system using a new 3D position and orientation (pose) estimation method with dual-eye camera that exploits the parallactic nature that enables reliable 3D pose estimation in real-time, named as 'Real-time Multi-step Genetic Algorithm (RM-GA).' We confirmed ROV have conducted docking that assumes charging battery under water by the system, having shown it effective. As a next step, docking experiment using the new ROV were conducted to verify the proposed system apply for new ROV. But, the new ROV is different from a ROV that have used previous experiments, on the point of thruster setting structure. Then, a new control system using Jacobian that shows relationship voltage and velocity was constructed. After it is confirmed the system is effective, docking experiments in the pool have been conducted. In this report, the structure and result of experiments are reported in detail.