Abstract: The Malay Basin is a Cenozoic fault basin. The structural characteristics and tectonic mechanism of the Basin are studied in this paper in order to understand the control of structure over hydrocarbon accumulation. The basin has experienced three evolutionary stages: the Eocene fault depression stage, the Oligocene depression stage, and the Miocene tectonic inversion stage. In Middle-Late Miocene, a positive inverted structure is observed with a gradual change from left lateral rotation to right lateral rotation. The inverse is stronger in the center and southeastern parts of the Basin. The trap formation time is earlier in the southern part of the Basin. Oil accumulated in the south and escapes to the north in the early stage; and gas generated in the later stage and effectively accumulated in the north. The source rocks in the north were formed under a rapid sedimentation rate in a large depth and conducive to a mature and gas phase. Due to the later uplifting of the southeast part of the basin, hydrocarbon generation is suppressed and there is less gas accumulation. Oil fields are mainly distributed in the southeast, and gas field in the north. In this paper, the Malay Basin is divided into six exploration areas, and the southeast, the main producing area extruded anticline oil area is the richest one. The deep H and J groups located in the overpressure belts are recommended as future exploration targets.