In this paper, for the over-actuated Autonomous Underwater Vehicle (AUV) system, a novel tracking controller with thruster fault accommodation is proposed. Firstly, a cascaded control method is proposed for AUV robust tracking control. Then, we deal with the tracking control problem when one or more thrusters are completely or partly malfunctioning. Different control strategies are used to reallocate the thruster forces. For the cases that thrusters are partly malfunctioning, a weighted pseudo-inverse is firstly used to generate the normalised thruster forces. When the normalised thruster forces are out of maximum limits, the Quantum-behaviour Particle Swarm Optimisation (QPSO) is used for the restricted usage of the faulty thruster and to find the solution of the control reallocation problem within the limits. Compared with the weighted pseudo-inverse method, the QPSO algorithm does not need truncation or scaling to ensure the feasibility of the solution due to its particle search in the feasible solution space. The proposed controller is implemented in order to evaluate its performance in different faulty situations and its efficiency is demonstrated through simulation results.