Methane gas hydrate related bottom-simulating reflectors (BSRs) are imaged based on the in-line and cross-line multi-channel seismic (MCS) data from the Andaman Forearc Basin. The depth of the BSR depends on pressure and temperature and pore water salinity. With these assumptions, the BSR depth can be used to estimate the geothermal gradient (GTG) based on the availability of in-situ temperature measurements. This calculation is done assuming a 1D conductive model based on available in-situ temperature measurement at site NGHP-01-17 in the study area. However, in the presence of seafloor topography, the conductive temperature field in the subsurface is affected by lateral refraction of heat, which focuses heat in topographic lows and away from topographic highs. The 1D estimate of GTG in the Andaman Forearc Basin has been validated by drilling results from the NGHP-01 expedition. 2D analytic modeling to estimate the effects of topography is performed earlier along selected seismic profiles in the study area. The study extended to estimate the effect of topography in 3D using a numerical model. The corrected GTG data allow us to determine GTG values free of topographic effect. The difference between the estimated GTG and values corrected for the 3D topographic effect varies up to ∼5 °C/km. These conclude that the topographic correction is relatively small compared to other uncertainties in the 1D model and that apparent GTG determined with the 1D model captures the major features, although the correction is needed prior to interpreting subtle features of the derived GTG maps.