Understanding the evolution of the basin and tectonostratigraphy is the key role to reveal all geological aspects and potential hydrocarbon resources. Northeast Borneo has many hydrocarbon resources especially in Mahakam delta. However, Berau sub-basin remains unclear due to lack of G&G data. This paper presents a new concept of tectonostratigraphy and basin evolution based on subsurface and surface data integrated with thin section as well as radiolaria analysis to determine the age of such basin. Present-day aerogravity data shows that Berau sub-basin has two depocenters trending N-S and E-W and is bordered by Mangkalihat High (MKH) in the south and Rajang Embaluh Group (REG) in the west area. The metamorphic belt in REG area was formed in Early Jurassic (190 Ma), meanwhile in MKH, the ophiolite sequence was formed during Middle-Late Jurassic based on the presence of Holocrptocanium sp. in chert interbedded with mudstone. Based on the analysis, Berau sub-basin experienced subduction to obduction during Early Jurassic to Late Jurassic. In Cretaceous, Berau sub-basin is filled with conglomerate, shale and quartz sandstone of Telen and Benggara Fm. that has provenance from MKH and REG area. In Paleogene, major breakup unconformity can be seen on the seismic section and spread across the basin overlaid by shale with tuff of Eocene-Oligocene Sembakung Fm. The deposition of Sembakung Fm is controlled by extensional regime caused by subduction rollback in NW Borneo. The carbonate sequence has dominated this area in Late Oligocene to Early Miocene. Following the collision of Kuching high in Middle -Late Miocene, the deposition was dominated by deltaic sediment due to regional regression phase. In Plio-Pleistocene period, Berau sub-basin consists of carbonate and deltaic sediment from Domaring and Sajau Fm. In this time structural reactivation and inversion due to transpressional system with SE-NW pattern had controlled Berau sub-basin. Based on the evolution of Berau sub-basin, four hydrocarbon plays are identified in this paper, Mesozoic Play especially in Telen Fm, Paleogene Carbonate Play in Tabbalar & Birang Fm, Middle Miocene Play especially in Latih Fm and Plio-Pleistocene Play in Sajau Fm and Labanan Fm. Working petroleum system in the basin manifested by many oil seeps that can be found in surface and postmortem of several wells data shows commercial to sub-commercial and abundant oil and gas show.