We analyzed the tectonics and stratigraphy of the Southern Great Tarakan Basin to determine its tectonic evolution during the Mesozoic-Cenozoic Eras, the evolution of basin geometry, and the potential of hydrocarbon using integrated surface and subsurface data. Southern Great Tarakan Basin can be divided into three sub-basins, Berau, Muara, and South Tarakan. They comprise deposits of Jurassic to Quaternary age, which can be assigned five mega sequences based on their lithological characteristics and tectonic development. We divide the tectonic events into four main phases; (1) contractional Jurassic-Cretaceous, (2) extensional Paleogene, (3) subsidence Early Neogene, and (4) contractional Late Neogene. The development of the strike-slip activity influenced the geometric evolution of the two sub-basins. NW-SE transpressional structures formed during the contraction phase caused most of the existing structure in Paleogene reactivated and inverted, followed by basement uplift and erosion. Consequently, the evolution of the transpressional system caused The Great Tarakan Basin to be divided into five sub-basins during the Late Miocene-Pliocene. Moreover, five horizons with hydrocarbon potential exist in the southern part of The Greater Tarakan Basin; three plays in the Berau Sub-basin, and two main plays in the Muara Sub-basin. The Late Neogene structures in the Berau Sub-basin control the accumulation, migration, and trapping mechanism, whereas these structures do not exist in Muara; hence, this sub-basin is dominated by stratigraphic traps.