Investigating the provenance evolution of sedimentary basins with complex tectonic histories is challenging because of the continuously evolving tectonic framework and changing source areas. Pearl River Mouth Basin (PRMB) in the northern South China Sea preserves a large volume of Cenozoic sediments derived from both intrabasinal and extrabasinal sources. However, rare study has been conducted to investigate the provenance evolution of the western PRMB. In this study, we report new detrital zircon U–Pb geochronological and heavy mineral data from the western PRMB, attempting to identify its potential sources and provenance evolution from Eocene to early Miocene. Our data from distinct structural units and formations reveal spatial-temporal differences in provenance. In the northern part, a similar age pattern with a major peak at ∼425 Ma and a subordinate peak at ∼230 Ma is preserved in the Eocene-late Oligocene sediments and suggests that sediments were mainly derived from the Yunkai Massif via Nanduhe River. By contrast, in the southern part, the Eocene-late Oligocene sediments display a dominant age population ranging from 100 Ma to 300 Ma, which implies that the sediments were mainly eroded from nearby Shenhu Uplift and Hainan Island. The heavy mineral data also record such spatial differences in provenance. However, during the early Miocene, the northern and southern parts show similar detrital zircon age patterns with multiple clusters at ∼245 Ma, ∼450 Ma, ∼850 Ma, 970–980 Ma, 1825–1845 Ma, and ∼2500 Ma, indicating that the Miocene sediments across the whole basin were mainly provided by the Pearl River system. The increase of Paleozoic and Precambrian zircons in the lower Miocene sediments suggests a profound provenance shift from multiple nearby sources to the South China Block via the Pearl River between Oligocene and Miocene in the western PRMB, and its timing is posterior to other regions of the PRMB. Finally, four-stage source-to-sink evolution for the PRMB is proposed, showing that sediment provenance in the PRMB is controlled by regional tectonic movement, drainage evolution, and basin architecture. This study suggests that the small-scale drainage system Nanduhe River sourced by Yunkai Massif contributed significantly to the PRMB between Eocene and Oligocene, and highlights its complex processes of provenance evolution that are relevant to the evolution of marginal sea basins globally.