The Miocene Sanya, Meishan, and Huangliu formations in the Qiongdongnan Basin (QDNB) record a complete evolutionary history of submarine fan systems, yet a continuous Miocene-scale depositional framework has not been established for the Northern Lingshui Sag. Using 3D seismic data, this study investigates the paleogeomorphological reconstruction, channel system architecture, channel-sink correspondence, and controlling factors of Miocene submarine fans within the Northern Lingshui Sag, QDNB. Paleogeomorphological reconstruction reveals three fundamentally different slope configurations. The Sanya Formation is characterized by a gentle ramp-like slope (1–2°) with high accommodation. The Meishan Formation exhibits a steep structurally partitioned slope (eastern part ~9°, western part 8° decreasing to 2°) with a confined trough in the east. The Huangliu Formation shows a mature moderate slope (3–4°) with reduced structural confinement. Channel system architecture shows fifteen NW-SE oriented channels in the Sanya, six N-S oriented channels in the Meishan, and seven bidirectional channels in the Huangliu. Channel-sink correspondence is strong in the Sanya, localized in the Meishan, and weak in the Huangliu. Fan evolution was driven by three controlling factors: relative sea-level fluctuations, sediment supply and provenance, and paleogeomorphology. Global eustatic falls at 23.0 Ma (T60), 15.5 Ma (T50), and 10.5 Ma (T40) facilitated fan development within lowstand systems tracts. The Ningyuan River supplied sand-rich sediment to the Sanya, the Lingshui River supplied mud-rich sediment to the Meishan, and dual Ningyuan and Lingshui rivers supplied low-flux mud-dominated sediment to the Huangliu. Two major transitions are identified: the Sanya-to-Meishan transition (ca. 15.5 Ma) represents channel reorientation from NW-SE to N-S, reduction from fifteen to six channels, and shift from sand-rich to mud-rich supply; the Meishan-to-Huangliu transition (ca. 10.5 Ma) represents channel reorientation from N-S to bidirectional, increase from six to seven channels, and shift from mud-rich to low-flux mud-dominated supply.