Autonomous Underwater Vehicles (AUVs) equipped with Side-Scan Sonar (SSS) play a critical role in seabed mapping, where precise navigation data are essential for mosaicking sonar images to delineate the seafloor’s topography and feature locations. However, the accuracy of AUV navigation, based on Strapdown Inertial Navigation System (SINS)/Doppler Velocity Log (DVL) systems, tends to degrade over long-term mapping, which compromises the quality of sonar image mosaics. This study addresses the challenge by introducing a post-processing navigation method for AUV SSS surveys, utilizing Factor Graph Optimization (FGO). Specifically, the method utilizes an improved Fourier-based image registration algorithm to generate more robust relative position measurements. Then, through the integration of these measurements with data from SINS, DVL, and surface Global Navigation Satellite System (GNSS) within the FGO framework, the approach notably enhances the accuracy of the complete trajectory for AUV missions. Finally, the proposed method has been validated through both the simulation and AUV marine experiments.