The embodiment of the invention discloses an accelerator control method and an accelerator control system based on a programmable gate array FPGA. The system comprises an output circuit; wherein the output circuit is in signal connection with an input circuit; an optical fiber triggering output circuit, wherein the optical fiber triggering output circuit is in signal connection with the output circuit; a power supply, wherein the power supply is in signal connection with the optical fiber triggering output circuit so as to provide variable voltage; a field programmable gate array circuit, wherein the field programmable gate array circuit is in signal connection with the optical fiber triggering output circuit so as to control triggering a time sequence control circuit to receive the time sequence of synchronous signal input, magnetron trigger enable, electron gun trigger enable, high-voltage discharge and ultra-low dose mode. The method has the advantages that the FPGA uses special logic processing hardware, the speed is high, and processing paths are parallel; the FPGA can be reconfigured, the same hardware can be reconstructed according to different tasks, and the flexibility ofthe using mode is nearly infinite; the FPGA can configure I/O quantity and function as required.