Hydrocarbon exploration in the deep-water area of the South China Sea is increasingly important. However, the Eocene strata, which are the primary source rock in the deep-water area of the Pearl River Mouth basin (PRMB), are poorly understood. This article studied the geological characteristics and hydrocarbon potential of the Eocene source rocks in the Baiyun Depression, which is the biggest and most important depression in the deep-water area of the PRMB. In the Eocene, the Baiyun Depression was an asymmetric rift basin that was controlled by the north-dipping detachment faults. A big freshwater lake existed in the study area and a huge delta developed in the northern gentle slope. The delta source rocks had higher total organic carbon and were greatly controlled by terrigenous organic matter input. They were type III kerogen and were likely to produce gas during maturation. The lacustrine source rocks were widely distributed in the center and south and had a higher hydrogen index (HI). They had both terrigenous and aquatic organic matter inputs. The kerogen was type II to III. They could produce both oil and gas during maturation. The Eocene source rocks were widely distributed in the Baiyun Depression. They had a huge thickness and high organic matter abundance. The organic matter had enough maturity to generate hydrocarbon from 18.5 Ma to the present. Therefore, the Eocene source rocks can provide sufficient hydrocarbon resources for deep-water petroleum accumulations and gas hydrate formations in the deep-water area of the PRMB.