The Qiongdongnan Basin (QDNB), located in the north of the South China Sea, is a Cenozoic rift basin with abundant oil and gas resources. Large flake hydrates have been found in the core fractures of Quaternary formations in the deep-water depression of the QDNB. In order to understand the spatial distribution patterns of these fractures, their geneses in sedimentary basins, and their influences on gas migration and accumulation, such fractures have been observed using high-resolution 3D seismic images and visualization techniques. Four types of fractures and their combinations have been identified, namely bed-bounded fractures/microfaults, unbounded fractures, fracture bunches, and fracture clusters. Bed-bounded fractures/microfaults are mainly short and possess high density; they have developed in mass transport depositions (MTDs) or Meishan and Sanya Formations. The unbounded fractures/microfaults that occur in Miocene–Pliocene formations are mainly long and discrete, and are dominantly caused by strong tectonic movements, the concentration of stress, and sustained intense overpressure. The fracture bunches and fracture clusters that occur in Oligocene–Early Miocene formations have commonly developed with the accumulation of large numbers of fractures and may be related to the release of pressure, diapirs, and basement fault blocks (228.9 ± 1 Ma). In this study, six fluid charging or leakage models are proposed based on distinct fracture types, assuming the uniform conductivity of each fracture. In a 3D space view, a vertical decrease in the fracture scale (number or density) will more likely result in gas supply than dispersion, thus promoting the accumulation of gas in the reservoirs. Nevertheless, the fractures above the Bottom Simulating Reflect (BSR)/seismic anomaly are excessively developed, and bed-bounded fractures within a particular layer, such as MTDs, can easily cause seabed leakage. These results are useful for explaining the vertical migration of gas/fluids in areas and formations with less developed gas chimneys, faults, diapirs, and other structures, particularly in post-rifting basins.