The traditional Gravity-Geologic Method (GGM) is an approach that combines shipborne bathymetric data and marine gravity anomalies data to invert seafloor topography by resolving short-wavelength gravity anomalies using the Bouguer plate formula. To further enhance the accuracy of GGM in seafloor topography inversion, an Improved Gravity-Geologic Method (IGGM) has been developed in this paper. A weighting parameter was introduced into the Bouguer plate formula, and short-wavelength gravity corrections were calculated at control points to refine the long-wavelength gravity field modeling further. A seafloor topography model with a spatial resolution of 1′×1′ was constructed for the reef area near the Nansha Islands (112°E—116°E, 8°N—12°N) using the Improved Gravity-Geologic Method. The accuracy of the model was evaluated using shipborne bathymetric data provided by the National Oceanic and Atmospheric Administration of the United States (NOAA). Results indicate that the IGGM model more accurately reflects fine topographic variations, with the standard deviation of 175.68 m in depth differences from measured data, representing a reduction of 7.01 m, 20.67 m and 19.68 m compared to the GGM model, the SIO V25.1 model and the SRTM15+V2.0 model, respectively. Compared to the GGM model, the IGGM model shows a significant accuracy advantage in complex reef areas with depths ≤1000 m, reducing the standard deviation of depth differences by 10.20 m. This validates the effectiveness of the Improved Gravity-Geologic Method in enhancing inversion accuracy, especially in reef regions, where it more accurately reflects the trend of seafloor topography changes, providing essential support for seafloor topography modeling in these areas.