Autonomous Underwater Vehicles(AUVs) have become an important tool for various purposes in subsea: inspection, recovery, construction, etc., and the development of autonomous control system is luglay desirable- thete zffe many problems associated with designing the control system for AUV due to unknown underwater envimn-Tnent, the possibility of subsystem failures, and unpredictable changes in the dynamics of the vehicle. In this paper, an autonomous control system based on the intelligent control theory to enhance operation efficiency of the ALTV is presented. The control system has a hierarchical structure which consists of mission planning level, mission control level, navigation level, and execution level. The performance of the control system is investigated by computer simulation. The results show that the proposed control system can be applied successfully to the AUV in spite of the possibility of failures in the vehicle and the collision hazard in the sea environment.