The invention discloses a code capturing method based on dual-FFT frequency domain filtering. The method comprises the steps of (1) performing down-conversion on received medium-frequency signals; (2), dividing baseband signals into Qms data, respectively multiplying by the complex conjugate of the threshold of the local code frequency and then performing Fourier inversion; (3), processing in periods; (4) performing fast Fourier transform; (5) lowpass filtering; (6) performing fast Fourier inversion on the filtered frequency domain signals; (7) performing coherent integration on the obtained signals and constructing a judgment statistics; (8) threshold judging and if the signal is larger than the threshold, judging that the signal is a detection signal. The signal passing a PMF is enabled to pass a lowpass filter firstly to filter the frequency outside a useful signal band, and then the filtered signal is subjected to reconstructing, so the noise is effectively filtered, the signals are subjected to non-coherent integration, the signal to noise ratio of the signals is improved to a greater extent, and the detection probability is improved.