The Late Cenozoic provenance study of the Pearl River Mouth Basin (PRMB) holds significant implications for understanding the tectonic-climatic interactions, drainage evolution, and oceanic circulation in the northern South China Sea. However, the Miocene sediment routing system remains poorly understood due to the paucity of zircon geochronological data and the effects of sediment mixing and homogenization. This study reconstructs the ancient source-to-sink system by means of detrital zircon analyses from the northern PRMB and zircon age-based mixture modeling of well-defined provenance end-members. The results disclose varied and complex source-to-sink scenarios since the Early Miocene, involving three primary contributors: the Pearl River drainage system, coastal SE China, and Taiwan Island. In combination with seismic facies and climatic proxies, the intensive addition of Precambrian zircons suggests that, during the Middle and Late Miocene, progressive drainage expansion within the Yangtze Block likely contributed to the increasing sediment supply from the western Pearl River drainage system. Furthermore, the provenance shift in the northern PRMB, as indicated by the Mesozoic ages, may reflect a response to the activation of oceanic circulation and intensification of the East Asian monsoon. Additionally, though less significant, contributions from the Hainan and Luzon Island are also observed, indicating the input of the branch of the Kuroshio Current during the Late Miocene.