The Pearl River Mouth Basin is a significant petroliferous basin formed on a pre-Cenozoic complex folded basement at the continental margin of South China. Although previous studies have extensively investigated the structural characteristics and hydrocarbon accumulation in the basin, considerable controversy remains regarding the structural attributes and basin-controlling mechanisms of the NW-trending blind basement faults. Based on integrated gravity-magnetic data, well-seismic data, and field geological surveys in South China, this study employs a land-sea collaborative research approach to systematically identify and define three major NW-trending blind fault zones in the Pearl River Mouth Basin (Guigang–Yangjiang–Yitong, Huaiji–Huizhou–Beiweitan, and Lianzhou–Lufeng–Dongsha fault zones) and establish their geometric developmental models. The research indicates that: (1) The NW-trending blind fault zones exhibit distinct spatial distribution patterns. Onshore, they are characterized by fault zones, stratigraphic dislocation, and large-scale drainage systems, while offshore, they show strong correlations with gravity-magnetic anomalies, basement lithology, sag structural features, and high CO2 concentration distributions. (2) The activity of the blind faults can be divided into three main stages: formation (Indosinian movement), transformation (Yanshanian movement), and reactivation (Himalayan movement). (3) Based on the degree of control exerted by the blind faults on sag evolution, three differential evolutionary models of sags are established: multi-fault joint control (transcurrent-composite transtension), single-fault strong control (restricted transtension), and weak-fault extension control (segmented transtension). (4) The control of NW-trending blind fault zones on sag evolution and source rock distribution significantly influences hydrocarbon migration, accumulation, and resource potential. The exploration discovery of the Huizhou 19-6 oilfield confirms the important controlling role of NW-trending fault zones in hydrocarbon enrichment. In summary, this study systematically reveals for the first time the developmental characteristics and evolutionary history of the NW-trending blind fault zones in the Pearl River Mouth Basin, further deepening the understanding of the basin’s tectonic evolution and providing important guidance and reference for petroleum exploration in the northern South China Sea.