Remotely Operated Vehicles (ROV) is playing an increasingly important role in the process of human exploration of the ocean, and its motion control system needs to be stable, reliable, rapidly responsible and easy to use. This paper designs and implements a new type of motion control system for ROV. The architecture of control system includes QT upper controller to input motion control instructions and display the status information, companion machine Raspberry PI used as a communicate transfer station, and runs the designed control method, bottom controller MCU for controlling the speed of motors and receiving sensor data and sending them upward. Meanwhile the kinematics and dynamics model of ROV are established. Then, the model-based PID controller of depth and three attitude angles in YPR-model is designed and implemented. Its performance is verified by simulation in MATLAB. Finally, in swimming pool the experiment of depth and three attitude angles control using model-based PID and model-free PID are conducted and compared. Through experimental analysis, the practicability, stability and reliability of the motion control system and the model-based PID control method are verified.