The invention provides an FPGA-based flux gate micro signal detecting system and an FPGA-based flux gate micro signal detecting method. The FPGA-based flux gate micro signal detecting system comprises a detecting module, an output module and a processing module which is realized by FPGA, wherein the detecting module converts a flux gate signal to a digital signal and transmits the digital signal to the processing module. The processing module performs processing for obtaining a secondary harmonic signal and transmits the secondary harmonic signal to the output module. According to the FPGA-based flux gate micro signal detecting method, after power amplification is performed on a sine wave with frequency of f0/2, saturation activation is performed on the activation coil of a flux gate sensor for generating a flux gate signal with frequency of f0. After filtering and analog-to-digital conversion are performed on the flux gate signal, cross-correlation detection is performed on the obtained digital signal and two reference signals for obtaining a secondary harmonic signal, the amplitude and the phase of the secondary harmonic signal. Finally digital-to-analog conversion is performed on the secondary harmonic signal, and the obtained analog signal drives the load to operate. According to the FPGA-based flux gate micro signal detecting system and the FPGA-based flux gate micro signal detecting method, related operation is realized by means of the FPGA. The FPGA-based flux gate micro signal detecting system and the FPGA-based flux gate micro signal detecting method have advantages of effective hysteresis reduction in signal transmission, high noise inhibition capability, convenient signal processing, and high measurement accuracy. Furthermore the FPGA-based flux gate micro signal detecting system and the FPGA-based flux gate micro signal detecting method can detect nanovolt-grade weak signals.