To reduce the influence of Doppler frequency to the weak global navigation satellite system (GNSS) signal acquisition and enhance GNSS signal detection performance, this paper proposes a novel method based on the differential correlation and fast Modified double block zero padding (FMDBZP) algorithm. The proposed algorithm involves using an improved Modified Generalized Differential Combination (IMGDC) to get the fine Doppler frequency estimation, then, compensate the performance loss on the FMDBZP caused by the Doppler frequency. Theoretical analysis and numerical simulation show that the acquisition sensitivity of proposed algorithm outperform the FMDBZP method about 1.2 dB while compared with the other mentioned differential algorithm it shows a good stability and frequency estimation accuracy.