In this paper, a FPGA-based GPS synchronous signal generator for the calibration of MT instrument is presented. Under the control of AT91RM9200 processor, five square wave signals with specific frequencies of 0.09375, 0.2344, 2.5, 20 Hz and 24 Hz for calibration can be generated, and are synced with GPS's PPS. Multiple frequencies calibration is all done at the same time due to the nature of square wave composed of extensive odd harmonics. We designed a SPI interface to realize the communication between FPGA and AT91RM9200. The soft IP processor PicoBlaze, as the control center inside FPGA, is employed to analyze and process the control parameters, and to control the synthesis of frequencies and their synchronization to the rising edge of PPS. The synthesized square signal is transmitted to the analog channel board through photon-coupled isolator. As the test result proves, the signal generator works well, and calibration signals have a lag of less than 1.5μs to the rising edge of PPS, more-than-10 MHz bandwidth and stable amplitude, which meets the calibration requirement.