The deeply buried reservoirs of Wenchang Formation in the Lufeng Depression, Pearl River Mouth Basin, display strong heterogeneity, and the major controls for the development of high-quality reservoirs remain unclear. To address these issues, we conducted a series of experiment analyses, including petrographic microscope, scanning electron microscopy, and X-ray diffraction, and analyzed the impacts of sedimentation and diagenesis on the quality of deeply buried reservoirs. The results demonstrate that the sandbodies of subaqueous distributary channel and mouth bar deposited in lowstand systems tract (LST) and highstand systems tract (HST), as compared to the beach-bar and subaqueous fan sandstones deposited in transgressive systems tract (TST), have coarser grain size, higher quartz content, and lower muddy matrix content, which induced stronger anti-compaction capability, higher preservation of intergranular pore spaces, and thus better reservoir qualities. The reservoir types developed in subaqueous distributary channel and mouth bar are mainly types I, II, and III with medium-low porosity and low-ultra low permeability, while beach-bar and subaqueous fan mainly developed type III reservoir with low-porosity and ultra-low permeability. The reservoirs developed in E2w of the study area have undergone strong compaction, intense dissolution, but weak cementation. The subaqueous distributary channel and mouth bar reservoirs in LST are adjacent to Ew4 source rock in spatial distribution, resulting in strong organic acid dissolution, and developed numerous dissolved pores. The charging of hydrocarbons before deep burial further inhibited the later compaction and cementation and protects the preservation of residual primary intergranular pores and secondary dissolved pores. The combination of these factors leads to the development of the abnormally high porosity and high-quality reservoirs in LST. The results of this study reveal the genetic mechanism of deep, high-quality reservoirs in the rift basin and guide the selection of high-quality reservoirs in the later stage.