Due to the continuous subduction of the paleo-oceans, there are many microplates in Southeast Asia with complex origins and tectonic evolution, which makes the paleogeographic reconstruction of the region extremely difficult, especially regarding the Northeast Borneo terrane of which the tectonic attribute and the pre-Cenozoic paleogeography remain highly controversial. The Baliojong Oceanic Plate Stratigraphy outcropped in Northeast Borneo is a precious material that documents the history of the spreading of the oceanic crust to its subduction and extinction. This study performs detailed provenance and geochronological investigations on two turbidite sections in the western part of the Baliojong Oceanic Plate Stratigraphy and integrates whole-rock geochemistry, mineralogy, and zircon U-Pb geochronology-morphology to determine the depositional ages and compositions, thereby revealing the subduction history and the paleogeography of the overlying plates. The results show that samples from the two sections are very different in terms of different provenance and geochronological proxies, with turbidites in the east (Section BF2) having younger sedimentary ages, higher compositional maturity and detrital content, mafic-dominated source composition, and more abundant and larger-sized zircon grains of the Caledonian and Indosinian ages than those in the west (Section BF5). These lines of evidence clearly indicate that the two turbidite sequences are the products of different periods of accretion. Combining the newly obtained proxies of the maximum depositional ages based on detrital geochronology and the published ages of radiolarian cherts and basalts, it is hypothesized that the two turbidite sequences were formed in the Late Cretaceous (~87 Ma and ~93 Ma). By comparing the zircon U-Pb age signatures of the Baliojong turbidites with those of source areas of the surrounding plates, we find that there is a potential provenance linkage to the zone of southern margin of the Indochina Plate-East Malaya-Northwest Borneo, and we hypothesize that the location of the subduction zone where the Baliojong Oceanic Plate Stratigraphy was formed was closer to Sundaland rather than South China. The Late Cretaceous paleogeography of Northeast Borneo revealed in this study is of great significance in reconstructing the Mesozoic subduction system of the South China Sea-Southeast Asia region.