Bathymetry data are usually obtained via single-beam or multibeam sounding;however, these methods exhibit low efficiency and coverage and are dependent on various parameters, including the condition of the vessel and sea state. To overcome these limitations, we propose a method for marine bathymetry inversion based on the satellite altimetry gravity anomaly data as a modification of the gravity-geologic method (GGM), which is a conventional terrain inversion method based on gravity data. In accordance with its principle, the modified method adopts a rectangular prism model for modeling the short-wavelength gravity anomaly and the Tikhonov regularization method to integrate the geophysical constraints, including the a priori water depth data and characteristics of the sea bottom relief. The a priori water depth data can be obtained based on the measurement data obtained from a ship, borehole information, etc., and the existing bathymetry/terrain model can be considered as the initial model. Marquardt's method is used during the inversion process, and the regularization parameter can be adaptively determined. The model test and application to the West Philippine Basin indicate the feasibility and effectiveness of the proposed method. The results indicate the capability of the proposed method to improve the overall accuracy of the water depth data. Then, the proposed method can be used to conduct a preliminary study of the ocean depths. Additionally, the results show that in the improved GGM, the density difference parameter has lost its original physical meaning, and it will not have a great impact on the inversion process. Based on the boundedness of the study area, the inversion result may exhibit a lower confidence level near the margin than that near the center. Furthermore, the modified GGM is time- and memory-intensive when compared with the conventional GGM.