In recent years, deep water areas have become popular exploration fields because of their abundant hydrocarbon resource potential. There are only relatively poor planar seismic profiles and no wells for deepwater areas of the Lingshui Formation in the Qiongdongnan Basin. A lot of faults developed and strata are fragmented due to high temperatures and high pressure, and this has resulted in dim sequence boundaries. Based on seismic data of the deepwater area and well data of bordering shallow water areas, Lingshui Formation was divided into four third class sequences; namely SI, SII, SIII and SIV, and the three-dimensional isochronous stratigraphic framework of the Lingshui Formation in the studied area was shaped. Based mainly on seismic attributes such as amplitude, continuity, internal structure and external shape, six typical seismic facies were identified, including mat-shaped, filling, wedge-shaped, foreset, moundy-shaped and lenticular-shaped, and a seismic facies distribution map was subsequently drawn. With studies on wells of bordering shallow water areas, regional sedimentary characteristics, and isopach map as references, sedimentary planar distribution features were analyzed. The deepwater area of the Lingshui Formation has mainly developed littoral and shallow sea. Sandstone bodies of fan delta, braided river delta, slope fan, basin floor fan, and turbidite fan are at an interdigitate junction to marine hydrocarbon source rocks and thus are favorable prospecting targets.