The present invention provides a high-voltage power electronic control device and a control method thereof. The device comprises an upper computer, an FPGA control module and a drive circuit. The upper computer outputs a signal to the FPGA control module. The FPGA control module generates a control signal according to the signal and outputs the control signal to the drive circuit. The drive circuit generates a drive signal according to the control signal, and outputs the drive signal to a to-be-controlled high-voltage power electronic device so as to control the on/off state of the to-be-controlled high-voltage power electronic device. The FPGA control module monitors the operating condition of the to-be-controlled high-voltage power electronic device and feeds back the monitoring data to the upper computer. The control function of the entire control device is realized based on the FPGA, so that the device is powerful in data processing capability. Meanwhile, the operating condition of the to-be-controlled high-voltage power electronic device is fed back to the upper computer. Based on the above feedback adjustment, the high-voltage electronic power device can be reasonably and effectively controlled.