The invention provides an FPGA experiment board debugging system, which comprises an FPGA chip, an input unit and a screen output unit which are arranged on the same printed circuit board PCB, wherein the FPGA chip is electrically connected with the screen output unit and the input unit inside the PCB. The FPGA experiment board debugging system further comprises a debugging and invoking unit, wherein the debugging and invoking unit is electrically connected with an FPGA to-be-debugged circuit and the screen output unit inside the PCB. Specifically, the FPGA chip is used for loading the FPGA to-be-debugged circuit; the debugging and invoking unit is used for sending a control signal to the FPGA to-be-debugged circuit, acquiring internal data generated after the FPGA to-be-debugged circuit runs the control signal, and transmitting the acquired internal data to the screen output unit; and the FPGA to-be-debugged circuit is used for operating according to the control signal. The FPGA experiment board debugging system can realize debugging without using external equipment, and can use an FPGA experiment board for debugging directly.