The invention belongs to an electromagnetic compatibility fault diagnosis method and particularly relates to an interference source identification method in a system-grade electromagnetic compatibility fault diagnosis. The interference source identification method is characterized by comprising the following steps of: step 101, utilizing positioning sensitive equipment; step 102, carrying out fault tree analysis on the positioning sensitive equipment; step 103, performing the fault tree analysis so as to obtain a priority level of a coupling path; step 104, testing to obtain interference testing data; step 105, storing the testing data into a database; step 106, obtaining a potential interference source through the fault tree analysis of the step 102; step 107, searching and determining the priority level of the interference source; step 108, combining the step 105 and the step 107 to identify the interference source; step 109, judging whether the interference source is a determined interference signal or not; if not, carrying out step 110; otherwise, carrying out step 111; step 110, carrying out environment monitoring; and step 111, obtaining the determined interference signal and finally, finishing the compatibility fault diagnosis. The interference source identification method in an electromagnetic compatibility fault diagnosis system has the advantages of convenience for use, short period, low cost and controllable faults.