In order to solve the problem of complex faults of radar and bottleneck problem in the expert system, a fault diagnosis system based on hierarchical fault tree and a new method of knowledge storage for radar is developed. The radar faults are divided into subjective faults and objective faults through the analysis of knowledge for some types of radar faults. Aimed at objective faults, a knowledge base structure based on polychromatic sets theory is proposed, which solves the problems of inconvenient storage of fault tree and lacking unified mathematical model, puts forward the description method of knowledge base and realizes the intelligent knowledge reasoning. Aimed at subjective faults, a knowledge base structure based on the method of conventional production rule is founded. The system is verified using VC++6.0. The result shows that knowledge bases with different methods are built respectively according to different types of faults, which improves efficiency and accuracy of the location of faults, providing a new way on the research of radar fault diagnosis system.