A system level methodology is presented for soft failure detection and analysis in small unmanned aerial vehicle (UAV) system, induced by radio frequency interference (RFI). This method includes a radio frequency test system based on the equivalent dynamic test method, and soft failure detection and identification method based on ground control station observation records and system log analysis. By designing signal forwarding system for global positioning system, the equivalent dynamic flight state of the UAV is realized. Through the application of standard radiated susceptibility test methods, the effects of RFI with multiple interference levels covering the frequency range from 2 MHz to 3 GHz on small UAV systems have been investigated. RFI is coupled into the UAV system through the antenna coupling and cable coupling. Soft failure modes are classified and failure analysis is mainly carried out through system log analysis, combined with full-wave simulation analysis, the root cause of the soft failure is determined. The understanding of the soft failure mode and susceptibility is beneficial to the design of UAV system, improving the robustness of software and hardware.