Abstract: Commercial-scaled oil and gas has not been discovered in the Zhu Ⅲ Depression of the Western Pearl River Mouth Basin in recent years. The Paleogene is the main exploration strata in the study area. However, its provenance system from the bottom up and sedimentary filling evolution law is unclear, which greatly hampered the new discoveries of large quality reservoirs and oil/gas fields in this area. Based on the sequence stratigraphic division, the third-order sequence of the Paleogene sedimentary period was taken as the basic unit of study, the regional geological background, Paleogene geomorphology, distribution of surrounding water system, heavy mineral assemblages, and rock thin sections were analyzed using structural geology, sedimentology, and other analytical methods. Result shows that there were two major provenance areas in the Zhu Ⅲ Depression during the Paleogene. One was the Shenhu uplift in the south, and its parent rock was magmatic rocks, shallow metamorphic rocks, and pre-Tertiary sedimentary rocks. The second was the provenance area covering the northern Hainan uplift, Guangdong-Guangxi uplift, and related river systems, and the parent rock was mainly magmatic rocks. The Eocene Wenchang Formation reflected a fault-rift scheme, represented by a thick semi-deep to deep water lacustrine delta deposit, being the main hydrocarbon source. The Early Oligocene Enping Formation to Late Oligocene Zhuhai Formation manifested a fault-depression scheme, characterized by evolving from a lake delta system to a coastal tidal flat delta system, respectively. This study provided guidance to the next exploration for large and quality reservoirs in the Zhu Ⅲ depression.