For regularly detecting large-scale sea-going freighter, oiler and so on and ensuring the security of harbor, channel, port and ship, based on independent research and development new marine underwater security detection robot, research and develop a multi-function and modular control system. The control system mainly includes water surface control and underwater control. The water surface control system uses host computer monitoring software based on MFC development, communicating with underwater control system of ARM9 as the core through telecommunication of umbilical cable. The main control chip of the underwater control system communicates with the slave controller (ARM-M0) through CAN bus, thus to control the thruster, mechanical arm and other peripheral devices. This paper applies an improved adaptive Kalman filter (AKF). By ROV underwater inspection, setting depth, setting heading and other experiments, the results show that AKF can get stable control and realize remote control for underwater robot.