Abstract: The Enping 20/21 Subsag in the Yangjiang Sag of the Pearl River Mouth Basin is a hydrocarbon-rich kitchen; however, exploration in the Paleogene has not yet achieved breakthroughs due to complex fault systems and unclear understanding of the genesis and reservoir-controlling mechanisms of the flower-like structures. Based on 3D seismic and drilling data, the evolution of the flower-like structures and their role in controlling hydrocarbon accumulation were studied. Results show that the structures were formed through three stages—the Wenchang, Enping, and Zhujiang-Hanjiang periods—under the combined effects of clockwise rotation of the regional stress field, magmatic diapirism, and left-lateral strike-slip along the Yangjiang-Yitong Ansha Fault Zone. The flower-like structures controlled the development of multiple fault-block traps. The fault system played dual roles of hydrocarbon migration and sealing: deep faults cutting into source rocks served as dominant migration pathways, while some other faults sealed effectively the traps. The “petal of the flower” zones contain fewer oil-source faults and have limited migration capacity, whereas “core of the flower” zones have high hydrocarbon concentration and the local migration conditions were favorable for the formation of large-scale reservoirs. Therefore, traps near the “core” zone shall be selected as the most promising exploration targets in the Paleogene of the areas.