The invention discloses a multi-FPGA system online updating method and system and computer equipment, the multi-FPGA system comprises at least two FPGAs, channel selection modules and storage modules, the second FPGA is connected with the corresponding storage module through the corresponding channel selection module, the first FPGA is connected with the corresponding storage module through the corresponding channel selection module of the second FPGA, and the first FPGA is connected with the corresponding storage module through the corresponding channel selection module of the second FPGA. The method comprises the steps that an upper computer specifies a first FPGA and a second FPGA; the first FPGA obtains the update data from the upper computer, switches the channel selection module corresponding to the second FPGA to the first channel, and then sends the update data to the corresponding storage module through the first channel; the first FPGA sends an instruction to the second FPGA, the channel selection module corresponding to the second FPGA is switched to the second channel, and the second FPGA obtains the update data from the storage module through the second channel and updates the update data. According to the invention, more efficient and flexible online updating is realized.