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Abstract The bathymetry under the Amery Ice Shelf steers the flow of ocean currents transporting ocean heat, and thus is a prerequisite for precise modeling of ice‐ocean interactions. However, hampered by thick ice, direct observations of sub‐ice‐shelf bathymetry are rare, limiting our ability to quantify the evolution of this sector and its future contribution to global mean sea level rise. We estimated the bathymetry of this region from airborne gravity anomaly using simulated annealing. Unlike the current model which shows a comparatively flat seafloor beneath the calving front, our estimation results reveal a 255‐m‐deep shoal at the western side and a 1,050‐m‐deep trough at the eastern side, which are important topographic features controlling the ocean heat transport into the sub‐ice cavity. The new model also reveals previously unknown depressions and sills that are critical to an improved modeling of the sub‐ice‐shelf ocean circulation and induced basal melting.