Aiming at the disadvantages of high fixing cost and partial observability of system environment in the process of repairing Autonomous Underwater Vehicle (AUV) software faults, a method was proposed based on micro-reboot mechanism and Partially Observable Markov Decision Process (POMDP) model for failure repair of AUV. To facilitate the implementation of the fine-grained self-repair micro-reboot strategy, a hierarchical structure was built based on micro-reboot combined with the characteristics of AUV software. Meanwhile, a self-repair model was put forward according to the theory of POMDP. With the goal of minimizing the fixing cost, the repair strategy was solved by Point Based Value Iteration (PBVI) algorithm to allow the repair action to execute in the partially observable environment at a lower cost.The simulation results show that the proposed repairing method can solve the AUV software failures caused by the software-aging and system calls. Compared with two-tier micro-repair strategy and three-tier micro-repair fixing strategy, this method is obviously superior to the contrast method in cumulative fault repair time and operational stability.