In order to solve the problem that the use of the existing automatic test equipment can not conduct the task of fault diagnosis very well, a design plan of fault diagnosis software system is proposed. Firstly, a fault diagnosis system framework and information model are given out. Then, taking electron warfare equipment complex test and fault diagnosis system in a certain type of aircraft as example, the function module design is described and a software system framework is built up. And this design plan is applied successfully to an electron warfare equipment complex test and fault diagnosis system in a certain type of aircraft, and good results are achieved, which shows that the plan is effective.