Cretaceous - Miocene sedimentary rocks of northern Borneo preserve records of subduction of the Paleo-Pacific and Proto-South China Sea, providing important evidence for reconstructing the tectonic evolution of Southeast Asia since the Mesozoic. However, the genesis and tectonic setting of these sediments remain controversial. In this study, new Sr isotope, combined with Nd isotope data were used to determine the provenance contribution of the Cretaceous – Late Eocene Lubok Antu mélange and the Rajang Group. Detrital zircon ages and sedimentary geochemistry data of the Cretaceous - Miocene strata are also used to better understand the tectonic evolution of Borneo. Results show that more than 60% of the sediments came from a magmatic belt during the Late Cretaceous to Early Paleocene, and more than 50% from the Malay Peninsula during the Paleocene to the Late Eocene. The proportion of different detrital zircon ages and sedimentary geochemical characteristics in Borneo changed from west to east during the Cretaceous to the Miocene, which may be related to drainage changes caused by the gradual closure of an ocean basin. Subduction ceased in central Borneo during the Early Paleocene, slightly later than Late Cretaceous cessation in western Borneo. The collapse of magmatic belt lead river drainages from the Malay Peninsula to flow into Borneo. Whereas subduction continued in Eastern Borneo until the Miocene. Opening of the South China Sea cut off the drainage from the Malay Peninsula, and the inner rocks in Borneo once again became the main source of sediments.