The invention discloses a full three-dimensional digital knowledge base system and an application method of a knowledge base. The knowledge base system comprises a flow control module, a specific knowledge design module, an interaction control module, an equation editing module, a search control module, a computing control module and a knowledge base small functional module and is an independent knowledge driving system capable of being hung on different CAD (Computer-Aided Design). The application method of the knowledge base can be applied to various fields such as products, processes, tool design, product inspection and the like in the mechanism manufacture industry. A designer expresses knowledge such as purposes, industry design specifications, standard manuals, design experience, computational formulas and the like through an open programming-free visual knowledge editing function and stores the knowledge into the knowledge base, a database and a model base for reusing; and wizard design is realized through parameter passing, data acquisition and interaction and platform interaction. The system has the advantages of strong generality, convenience and rapidness, no leakage of enterprise core technology experience knowledge and the like and provides means for technical innovation and knowledge and experience accumulation.