In order to improve the Remote Operated Vehicle (ROV) into a reliable and maintainable one, this paper has presented a fault tolerance control system structure. Its surface platform includes fault diagnosis and tolerance modules. In fault diagnosis module, a second order sliding mode observer has been built on the basis of its dynamic model, so as to diagnose the thrusters’ conditions through the residue of command quantity. Coresponding with its thrusters’ position, a force allocation model has been established to realize fault tolerable control. Based on duality priciple, the energy-like function concerning ROV control is established. On the basis of the energy-like function, the recurrent strategy has been deduced for thrust allocation when some of thrusters are found failure. Simulations and experiments have been made to verify and analyse the control system structure. They have proved the SY-II control architecture is a reliable control system, it can detect the thruster fault precisely, realize fault tolerable control.