The micro-grid is a relatively autonomous system with flexible topology and diverse operation mode. In order to solve the fault diagnosis problem resulted from the varied topology of micro-grid, this paper proposes a hierarchical Petri net diagnosis model. The micro-grid protection information is described with hierarchical protection set. And when the micro-grid topology changes, only the corresponding information of the protection sets need updating, instead of changing the whole model, so as to improve the adaptability to the flexible topology of micro-grid. The diagnosis model can effectively distinguish the misoperation of protection and circuit breaker, and deal with the sequential data come from the protection. In order to enhance fault tolerance of the diagnosis system, this paper uses intelligent weighted fuzzy Petri net and adaptive cumulative value to improve the accuracy of fault diagnosis. The effectiveness of the proposed method is verified by simulation example.