Autonomous Undenvater Vehicles (AUVs) are mobile platforms with excellent maneuverability, which are preferred for microscale and mesoscale ocean feature tracking in near real time mode. With their good maneuverability and low cost, AUVs make autonomy mobile observation of ocean dynamic process feasible and convenient. Aiming for the observation of the typical microscale and mesoscale oceanographic features near South China Seas, we give thorough discussion of control and tracking strategy with AUVs. Firstly, we give the composition of autonomy observation system, mainly including vehicle dynamic control, multi underwater vehicles path plan and data process. Secondly, considering the driving factors and variation properties of the ocean feature, we give the control and decision making strategy with underwater vehicles for ocean feature tracking. Lastly, with respect to different types of ocean feature, we give discussion of advantages and constraint conditions of the AUVs control and tracking strategy.