The study of deepwater channels is important for the understanding of the sedimentary evolution mechanism and the sedimentary process of the marginal sea. In 2019, thick pore-filling gas hydrate with high saturation was firstly discovered in the Quaternary sands of the Qiongdongnan Basin (QDNB), which expanded the reservoir types of gas hydrates in the South China Sea. However, the distribution of sand-related channels is not well characterized, which limits the ability to predict sand reservoirs with gas hydrate. Using integrated 2D/3D seismic, multi-beam, well logging, and coring data, the current study documents the distribution characteristics of channel systems in the Quaternary strata and discusses their controlling factors. The integrated analysis shows that the channel-related sedimentary facies include channel-filling facies, levee facies, crevasse splay facies, and lobes facies. A total of six periods of channel systems is identified in the Quaternary strata. There are obvious distribution differences between the Channel 1 and Channel 3 systems when comparing the western, middle, and eastern sections: the channels in the western and eastern sections are mainly dominated by near straight V-shaped channels, while the middle section mainly consists of large braided channels, where channel-levee sedimentary facies developed. Compared with the distribution of the Central Canyon that developed in the Miocene, the Channel 1 and Channel 3 systems in the western section show southward migration since the Miocene. The distribution and evolution of Quaternary channels were likely collectively controlled by seafloor morphology, tectonic movement, sea-level fluctuations, and provenance supply. Tectonic movement controls seafloor morphology, which directly controls the flow of channels and their distribution characteristics; provenance supply determines the scale and sedimentary characteristics of each channel. The periodic changes in sea-level determine the evolution of multi-stage channel systems. This study has implications for the prediction of gas hydrate–bearing sands in the Quaternary QDNB and deepens our understanding of the Quaternary tectonic and sedimentary evolution in the QDNB.