The invention discloses a method and system for checking and avoiding interference of a pseudo base station. The system for checking and avoiding interference of the pseudo base station comprises an input module, a detection module, a searching module, a judgement module, an execution module and a pseudo base station feature library. The input module carries out statistics on the performance statistics index and screens out bad quality areas; the judgement module screens out a suspected pseudo base station area according to switching between the bad quality areas; the searching module searchesthe updating condition of the suspected pseudo base station area and feature information in the pseudo base station feature library; the judgement module matches the searched updating condition of the suspected pseudo base station area with the feature information in the pseudo base station feature library, and judges whether the suspected pseudo base station is a pseudo base station; for the assertive pseudo base station, the execution module isolates the pseudo base station from the existing network, and checking and avoiding are completed. The pseudo base station can be recognized quicklyand accurately in batch, manual testing and on-site frequency sweep are not needed, time is saved, influence of the pseudo base station on the user perception and the network index is reduced to the hilt, and experience solidification is checked.