The invention discloses an online FPGA configuration file updating device of a three-dimensional acoustic logging instrument. An FPGA updating configuration file is generated by an integrated development environment; and a data sending module converts the FPGA updating configuration file into a network signal and the network signal is sent to a cable by an LAN port, so that generation, packaging and sending work of the FPGA configuration file is completed by an upper computer. A switching board uses a microprocessor to control data and receive the FPGA updating configuration file, carries outchecking, packaging, and checking bit adding, and then sends the FPGA configuration file to a control board through an McBSP interface. The control board determines whether the FPGA updating configuration file is used for updating an FPGA of the control board or FPGAs of collection boards and then analyzes the FPGA updating configuration file into a JTAG standard data stream. Therefore, online updating of the configuration file of the corresponding FPGA is realized.