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Autonomous underwater vehicle (AUV) is one of the most important exploration tools in the ocean underwater environment, whose movement is realized by the underwater thrusters, however, the thruster fault happens frequently in engineering practice. Ocean currents perturbations could produce noise for thruster fault diagnosis, in order to solve the thruster fault diagnostics, a possibilistic fuzzy C-means (PFCM) algorithm is proposed to realize the fault classification in this paper. On the basis of the results of fault diagnostics, a fuzzy control strategy is proposed to solve the fault tolerant control for AUV. Considering the uncertainty of ocean currents, it proposes a min-max robust optimization problem to optimize the fuzzy controller, which is solved by a cooperative particle swarm optimization (CPSO) algorithm. Simulation and underwater experiments are used to verify the accuracy and feasibility of the proposed method of thruster fault diagnostics and fault tolerant control.