The invention discloses a method and a system for capturing an aperiodic long code signal of a satellite navigation receiver. The method comprises the following steps: S1, in a rapid search stage, carrying out segmented correlation accumulation by using relatively short coherent integration time, carrying out rapid Fourier transform, envelope taking and post-accumulation processing on a segmented correlation value, and maximizing a frequency spectrum envelope to obtain a Doppler frequency initial estimation value under a current code phase; s2, a false alarm verification stage: accumulating a plurality of segmented correlation values after phase rotation in the fast search stage to obtain a segmented correlation value with longer coherent integral time, similarly performing fast Fourier transform, envelope taking and post-accumulation processing, performing capture judgment by using a spectrum envelope maximum value, and when the envelope maximum value exceeds a capture threshold, performing false alarm verification, outputting the current code phase and Doppler frequency as a signal capturing result. Under the condition that the Doppler search range is guaranteed, high detection performance can be achieved, and two-stage detection is achieved under the condition that correlator resources are not increased.