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The Borneo Accretionary Orogen (BAO) is located in a central position of SE Asia, surrounded by the long-lived westward subduction of the Pacific Plate, northward subduction of the Indian Plate beneath the Eurasian Plate and a passive continental margin of the South China Sea. Based on the previous studies in stratigraphy, structural geology and geophysics, a number of tectonic models on the BAO have been proposed, but these models do not perfectly match all of the geological facts. A field-based structural analysis of the rocks of Sabah in Malaysia has recognized that the deformation in Sabah can be divided into four episodes (D1-D4). The D1 deformation developed complete displacement foliation (S1) and NNE-trending thrusts. Then D1 structures were reworked by the subsequent D2 deformation. D2 deformation resulted in WNW- or NW-striking thrusts, followed by NNW-SSE-trending thrusts and folds (D3). Some NNE-trending sinistral strike-slip faults and WNW-trending dextral tension-shear faults (D4) offset the D3 structures. D1 is related to the collisional event in the Sabah Orogeny during 23-16 Ma, and D2 corresponds to the formation of the Deep Regional Uncomformity (DRU) at 16 Ma. D3 is related to the Shallow Regional Uncomformity (SRU) at 10 Ma. D4 is associated to the NW-SE-trending extension after the multi-stage collisional events. Analysis of the sedimentary and magmatic data reveals that the BAO is a Mesozoic and Cenozoic accretionary orogeny, represented by the intensely deformed Rajang-Crocker Group Accretionary prism, ophiolites and calc-alkaline igneous rocks. The accretionary orogen is related to the evolution of the Proto-South China Sea Ocean (PSCS). The PSCS continuously subducted under the Borneo Block and closed in the Late Eocene-Early Miocene time. The subduction zone of the PSCS retreated to the north in the Mesozoic and Cenozoic and migrated to the present-day Nansha Trough. The BAO is still active, as represented by a series of thrusting and subduction of the Dangerous Grounds under the Borneo Block. The NNE-trending subduction-related faults are considered as transform faults, rotating to the present-day NW-trending faults due to the anti-clockwise rotation of the entire Borneo Block. In particular, the previous NNE-trending Tinjar Fault is regarded as a major boundary in sedimentation and magmatism. To the NE of the fault, the strata and igneous rocks are Oligocene-Early Miocene, but to the SW of the fault, the strata and igneous rocks developed during the Cretaceous-Late Eocene interval. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]