Modeling of long-wavelength gravity anomaly is crucial for bathymetry inversion with a gravity-geologic method. We propose a new method, named as iGGM, to approximate the long-wavelength gravity anomalies by using a finite element method based on an adaptive triangular mesh which is constructed by uneven control points. The mesh size is suitably controlled to ensure that there are several control points in each grid. By using iGGM, the bathymetry in the South China Sea (Test Area #1: 112°E–119°E, 12°N–20°N) and East China Sea (Test Area #2: 125°E–130°E, 25°N–30°N) is estimated. The performance of the method was evaluated by comparing the predictions with Earth topographical database 1 (ETOPO1) model and shipborne depths in the test points. Results show that the depths derived by iGGM have a strong correlation with the shipborne depths. In the test points, the mean values of their differences are smaller than 10 m. The standard deviations of their differences are smaller than 120 m and their correlation is stronger than 0.98. Meanwhile, the results provided by the iGGM model are comparable with that obtained by the ETOPO1 model, e.g., the differences between iGGM and ETOPO1 models in test points for Test Areas 1 and 2 are 116 and 70 m in standard deviation, respectively.