Global Navigation Satellite System Reflectometry (GNSS-R) is a remote sensing technology that uses GNSS signals reflected over Earth’s surface, offering advantages such as high spatio-temporal resolution and cost-effectiveness. GPS navigation signals convey navigation information through the navigation bits, in which phase jumps occur randomly at 20 ms interval. However, navigation information is meaningless in GNSS-R and limits the coherent integration time. This study presents a technique to mitigate the impact of the navigation bits on the generation of DDMs by using the raw GNSS-R data from the Fengyun-3E (FY-3E) satellite. Sample results show that, after correcting for the navigation bits, the signal-to-noise ratio (SNR [dB]) of DDMs increased by ~0.4 dB over sea to up to 3 dB over sea ice, showing that this improvement is very significant for coherent targets. The proposed navigation bit correcting method in this study significantly improves the usability of these DDMs, and opens the door to other applications that require larger integration times.