The invention discloses a high-sensitivity satellite navigation signal capturing method and a system. The system comprises a digital down-conversion module, an average sampling and block accumulation module, an FFT (fast Fourier transform) module, a circumference shifting module, a local PRN (pseudo random noise) code FFT conjugate memory, a complex multiplier module, an IFFT (inverse fast Fourier transform) module, a differential coherence integration module, a peak detection module and a sequential control module. The digital down-conversion module realizes digital down-conversion operation for satellite digital intermediate frequency signals; the average sampling and block accumulation module averagely samples satellite data and completes a block accumulation function; the FFT module searches code phase frequency domains; the circumference shifting module utilizes Doppler circumference shifting search to replace frequency compensation; the local PRN code FFT conjugate memory stores a local PRN code FFT conjugate result; the complex multiplier module realizes signal de-spreading; the IFFT module calculates different code phase coherence results; the differential coherence integration module accumulates differential coherence energy of de-spread satellite signals; the peak detection module realizes signal capturing output; and the sequential control module controls timing sequence of the various modules of the system. Weak signal capturing speed and sensitivity of a satellite navigation receiver are improved, and parameters can be configured flexibly.