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The historical records of mechanical fault contain great amount of important information which is useful to identify the similar fault. The current fault diagnosis methods using historical records are inefficient to deal with intuitive application and multicomponent multiphase fault diagnosis. Towards the problem, the rapid and intelligent fault diagnosis method based on system-phenomenon-fault (SPF) tree is proposed. The method begins with the physical system of the fault system, conceives the fault causes as leaves, the fault causes as leaves and the frequentness of fault as the interrelationship, and finally forms the fault tree with structural relationship of administrative subordination and flexible multi-granularity components. Firstly, the forming method of SPF tree is discussed; Secondly some basic definitions as synonymous branch, the tough degree of the branch, the dominant leaf, and the virtual branch are defined; and then, the performances including the merger of the dominant branches keeping dominant, the merger of the synonymous branches keeping dominant were proved. Furthermore, the merging, optimizing and calculating of virtual branch of SPF tree are proposed, the self-leing mechanism including the procedure and the related parameter calculation is presented, and the fault searching method and main fault statistics calculation are also presented based on SPF tree. Finally, the method is applied in the fault diagnosis of the certain type of embedded terminal to demonstrate fault information searching in the condition of the synonymous branch, the virtual branch merging and visual presentation of search results. The application shows that the proposed method is effective to narrow down the scope of searching fault and reduce the difficulty of computing. The proposed method is a new way to resolve the intelligent fault diagnosis problem of complex systems by organizing the disordering fault records and providing intuitive expression and intelligent computing capabilities.