Marine gravity anomalies are crucial parameters and elements for determining coastal and ocean geoid, tectonics and crustal structures, as well as offshore studies. This study aims to derive and develop a marine gravity anomaly model over Malaysian seas from multi-mission altimetry data. Universiti Teknologi Malaysia 2020 Mean Sea Surface Model is computed based on along-track data from nine satellite missions, incorporating TOPEX, Jason-1, Jason-2, ERS-2, Geosat Follow on (GFO), Envisat-1, CryoSat-2, SARAL/AltiKa, and Sentinel-3A. The data exploited are from 1993 to 2019 (27 years). Residual gravity anomaly is computed using Gravity Software, and two-dimensional planar Fast Fourier Transformation method is applied. The evaluation, selection, blunder detection, combination, and re-gridding of the altimetry-derived gravity anomalies and Global Geopotential Model data are demonstrated. Cross-validation procedure is employed for data cleaning and quality control using the Kriging interpolation method. Then, cross-validation procedure is applied to the tapering window width 200, which adopting the GECO model denotes the optimum gravity anomaly with root mean square errors in the range of ± 4.2472 mGal to ± 6.0202 mGal. The findings suggest that the estimated marine gravity anomaly is acceptable to be implemented in the marine geoid determination and bathymetry estimation over Malaysian seas. In addition, the results of this study are valuable for geodetic and geophysical applications in marine areas.