This study used backstripping analysis, combined with a multi-proxy dataset comprising borehole logs, multichannel seismic surveys, high-resolution bathymetric data, and regional tectonic constraints to quantitatively reconstruct the paleobathymetric evolution of Prydz Bay. As the third largest bay in Antarctica, Prydz Bay is located in front of the Lambert Glacier-Amery Ice Shelf of the East Antarctic continental margin. Prydz Bay is covered by rich multi-channel seismic lines, and Ocean Drilling Program Leg 119 and 188 provided available lithology data of 8 boreholes, establishing it as an ideal area for basin analyses and paleobathymetric evolution. Core porosity data indicated that the sedimentary strata on the continental shelf are overcompacted due to grounded glacier loading, while the slope exhibits hemipelagic sedimentary characteristics. Considering the variability of deposition history and different crustal structure, the compaction was calculated separately between the continental shelf and slope. By comparison with previous studies, our new results quantitatively infer the thickness of sediment variations, and more detailed paleobathymetric grids were produced in different stages since Eocene-Oligocene boundary. The newly reconstructed paleobathymetry contributes to the understanding of the depositional response of ice sheet dynamics and ocean circulation changes, providing critical constraints on the coupled glacial-ocean-sediment system. Furthermore, spatially explicit gridded data could be used to establish more realistic regional ice sheet, ocean circulation, and climate models in the future.