A stereo-vision-based system of autonomous under-water vehicles (AUVs) for sea-bottom docking that enables for battery recharging to extend persistence time of underwater operation has been developed. This paper presents the docking experiment using a developed V-shaped-thruster typed under-water vehicle. A real-time 3 D pose (position and orientation) estimation method using a real-time multi-step genetic algorithm (RM-GA) has been proposed by the authors in previous works and used for docking based on 3D recognition a s a feedback pose information in real-time, named as 3D Move on Sensing (3D-MoS). Sea docking experiment results have confirmed the functionality and practicality of proposed docking approach using a hovering typed ROV in previous works. Since the hovering typed underwater vehicles are limited in mobilities concerning speed and operational space, verification of the 3D-MoS system using underwater vehicle that has more mobility deem to be meaningful direction for vision-based docking system to expand the utility value of AUVs. Therefore, in this study, control system for a new V-shaped-thruster typed vehicle is developed and docking experiment is conducted. This paper presents the development of the hardware design of V-shaped-thruster typed underwater vehicle and improvement of controlling with consideration of coupled configuration of thrusters.