The failure mechanism of Xilinx’s FPGA chip XC7A200T-2FBG676 under RF interference is studied. When RF interference injects into the power supply pins of the FPGA core, it is found that with the increase of interference intensity at the some frequencies, three types of FPGA failures occur successively, namely core failure, I/O failure and configuration failure. Test analysis and HSPICE simulation show that the core failure is due to the poor disturbance immunity of the logic layer of BRAM, the I/O failure is due to the simultaneous distortion of input/output signals under RF interference, and the configuration failure is due to the configuration system reading the wrong configuration enable signal. This study could provide guidance for the electromagnetic compatibility design of this kind of FPGA chip or system, as well as the formulation of electromagnetic immunity detection scheme of this kind of FPGA.