Aiming at the problem that it is difficult to realize the firmware upgrade method of FPGA by using JATG emulator in engineering application,a serial port online upgrade method based on Xilinx FPGA is proposed under the complex condition of the whole machine system.The FLASH is divided into Golden Image area and Update Image area by using MultiBoot function.The Golden Image area is used to store boot firmware and the Update Image area is used to store engineering application firmware.The experiment results show that the serial port rate identification error is less than or equal to 1.408% when the Update Image is upgraded,which has better baud rate adaptive capability,and can be applied to scenarios with unconventional baud rates.