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The emergence of the “Paleokarst play” as a promising prospect in the Penyu Basin’s Pre-Tertiary zone has become an interest in extending hydrocarbon exploration to the underlying “Pre-Tertiary basement” interval. Through the utilization of vertical gravity anomalies gradient and 3D density inversion modeling, quantitative insights into Pre-Tertiary carbonate geobodies have been attained. A 3D unconstrained map has identified four (4) potential Pre-Tertiary carbonates. Significant density contrasts among Tertiary sediments, Pre-Tertiary carbonates, and Pre-Tertiary sediments have been revealed through forward modeling along selected seismic profiles, enhancing existing seismic interpretations. The study suggests that the formation of these carbonates is linked to the development of a back-arc suture zone induced by the eastward subduction of the Palaeo-Tethys during the Late Carboniferous to Early Permian. This suture zone marks the boundary between Sukhothai’s Permian island-arc system and the western margin of the Indochina Terrane, indicating notable carbonate buildups closer to the suture zone areas due to dynamic tectonic activity, which elevated regional topography. These discoveries offer new perspectives on exploring the Pre-Tertiary intervals of the Penyu Basin, once considered merely a “basement” with unclear justification and doubt. Now, these areas present promising opportunities for further exploration and potential hydrocarbon discoveries.