The present invention discloses an online upgrade method for FPGA system implanted CPU inside, wherein the feature is implanting a cutting CPU with operating system running on it inside FPGA. The upgrade process comprises the following procedures: starting network driver module through loading boot program after post power on self test and initialization in FPGA; receiving network parameter from DHCP server and getting TFTP server address from DNS server; downloading upgrade document to SDRAM from server when user upgrade switch is detected open; writing FLASH chip after check. New system startup can be guided after successful upgrade. Simultaneous online upgrade for system software and hardware can be realized utilizing feature of programmable software and hardware of FPGA, and system expansibility and upgrade flexibility is improved through the invention.