The present invention relates to a method for remotely configuring and updating FPGA devices in a communication device. A general-purpose pin of the communication device CPU simulates the JTAG timing, and is connected with n to-be-programmed FPGA devices in a daisy-chaining manner. The FPGA devices are FPGA chips, PROMs, or CPLDs. The communication device is networked with the PC, a configuration and update file of the corresponding FPGA device is transmitted to an embedded web server in the communication device, the embedded operating system of the communication device receives the FPGA xsvf configuration file from the embedded web server and parses the file as a JTAG instruction, and finally configuration and update of the connected related FPGA devices are realized by controlling the electrical level and the timing on the JTAG bus stimulated by the general-purpose pin GPIO. According to the method provided by the present invention, remotely configuring and updating FPGA devices in the communication device can be realized without opening the chassis of the communication device, so that the maintenance and update of the communication device are greatly facilitated, and manpower and material costs are significantly saved.