AbstractThe Malay Basin is a mature hydrocarbon province currently being re‐assessed for CO2 storage. Selecting an appropriate storage site requires a comprehensive understanding of the structural and stratigraphic history of the basin. However, previous studies have been limited to observations from either regional 2D seismic lines or individual 3D seismic volumes. In this study, we access and utilise a basin‐wide (ca. 36,000 km2) 3D seismic and well database to describe the structural and stratigraphic features of the basin, particularly those within the uppermost ca. 4 km (Oligocene to Recent) and gain new insights into the basin's evolution. E–W transtensional rift basins first developed due to sinistral shear across an NW‐SE strike‐slip zone. The NW‐SE basin morphology seen today was generated during the late Oligocene–early Miocene, during which time dextral motion across marginal hinge zones created en‐echelon antithetic, extensional faults and pull‐apart basins, especially well preserved along the western margin of the basin. Collisional forces to the southeast during the early to middle Miocene resulted in the shallowing of the basin, intermittent connection to the South China Sea and a cyclic depositional pattern. Around 8 Ma (late Miocene), a significant uplift of the basin resulted in a major unconformity with up to 4.2 km of erosion and exhumation in the southeast. In the centre and northwest of the basin, the inversion of deeper E–W rifts resulted in the folding of Miocene sequences and the formation of large anticlines parallel to the rift‐bounding faults. The Pliocene to Pleistocene history is more tectonically quiescent, but some extensional faulting continued to affect the northwest part of the basin. Larger glacio‐eustatic sea‐level fluctuations during this time resulted in major changes in sedimentation and erosion on the Sunda Shelf, including the formation of a middle‐Pliocene unconformity. These structural events have created a variety of hydrocarbon traps across the basin of different ages, including transpressional anticlines, rollover anticlines and tilted fault blocks. Each of these has discrete and distinct trap elements with important implications for their CO2 storage potential.