As for the increasing complexity of AUV missions, more reliable and robust abilities of AUV system are required. After introducing the classical control system of AUV, the paper presents a layered self-healing architecture, and a mechanism based on micro-reboot which is applied to self-healing process. This work aims to develop an architecture on how to provide a stable and continued implementation of the mission after semipermanent failure occurred. The design of self-healing architecture and the generation process of micro-reboot plan are given.