In the distributed geophysical instruments, it would lead to reduced reliability, increased manufacturing costs and low efficiency problem when firmware program upgrade of the high-end FPGA for control data processing of master station in using traditional methods, the direct updating FPGA configuration Flash chip firmware program proposed based on researching on the ways of the update the FPGA program.Using FPGA chip and the FPGA corresponding Flash chip, it directly design the FPGA configuration FLASH model interface by the logic resource,through this interface and the external interface bus between FPGA and computer receives remote firmware program and send it to the configuration FLASH, then complete FPGA firmware updated.Verified by experiments by Xilinxs V6 series FPGA, the method to download a FPGA program takes about 2.5min, 10 times faster than other methods efficiency, avoiding the problems about use of third-party controllers disassemble and other methods to bring reliability, cost and technical complexity.This approach has a high practical significance.