The invention relates to a single-particle irradiation experiment test system and method based on a JTAG (joint test action group) interface. The test system comprises an upper computer and a test board, wherein the test board comprises an SRAM (static random access memory), a configuration PROM (programmable read-only memory), a control processing FPGA (field programmable gate array) and a tested FPGA, the control processing FPGA comprises a serial port communication module, a process control module, a tested FPGA configuration module, a JTAG read-back module and an SRAM read-write module, simple functions are loaded on the tested FPGA, the upper computer is in charge of flow process control and data processing, and the control processing FPGA is in charge of processing commands sent by the upper computer and carrying out work such as single-particle turning and single-particle function interruption detection. The system and the method have the advantages that the control processing FPGA is connected with the JTAG interface of the tested FPGA, the single-particle turning detection is realized through the JTAG interface, the system is more stable, the result is more reliable, in addition, the device model of the tested FPGA can be automatically recognized, and the effect of self adaptation to the single-particle irradiation experiment test of the tested FPGAs in different models is achieved.