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The wide range of bathymetry models can be estimated using the marine gravity information derived from satellite altimetry. However, due to nonlinear factors influences such as isostasy effects, the bathymetry estimated by gravity anomaly and vertical gravity gradient is not satisfactory. Therefore, to improve the accuracy of bathymetry estimation, a combined neural network and gravity information wavelet decomposition (CNNGWD) method is proposed based on wavelet decomposition and correlation analysis. Next, the bathymetry of the Manila Trench area is estimated using the CNNGWD method and multilayer neural network (MNN) method, respectively. Then, the shipborne sounding data and international bathymetric models such as ETOPO1 and GEBCO_2021 are separately used to evaluate the accuracy of the inversion models. The results show that the root mean square errors (RMSE) of the difference between the bathymetric model one (BM1) estimated by CNNGWD method and the shipborne sounding data is 59.90 m, the accuracy is improved by 12.45%, 64.70% and 28.68% compared with the bathymetric model two (BM2) which estimated by MNN, ETOPO1 and GEBCO, respectively. Finally, by analyzing the bathymetric accuracy shift with depth, the BM1 has lower RMSE at depths ranging from 1000 m to 3000 m. Furthermore, BM1 shows dominance in flat troughs and rugged ridge regions. [ABSTRACT FROM AUTHOR]