Ultra-deeply buried (>5000 m) marine carbonate reservoirs have gradually become important exploration targets. This research focuses on providing an understanding of the basic elements of the ultra-deeply buried Middle Triassic Leikoupo marine carbonate petroleum system within the Western Sichuan Depression, China. Comprehensive analyses of organic geochemistry, natural gas, and C–H–He–Ne–Ar isotope compositions suggest that the reservoir is charged with compound gases from four source rock units including the Permian Longtan, Middle Triassic Leikoupo, Late Triassic Maantang and Xiaotangzi formations. Approximately a 50-m thick outcrop and 100-m length of drilling cores were examined in detail, and 108 samples were collected from six different exploration wells in order to conduct petrographic and petrophysical analyses. Thin-section and scanning electron microscope (SEM) observations, helium porosity and permeability measurements, mercury injection capillary pressure (MICP) analysis, and wire-line logging (5,500–6,900 m) indicate that the reservoir lithologies include argillaceous algal limestones, dolograinstones, crystalline dolostones, and microbially-derived stromatolitic and thrombolitic dolostones. Reservoir properties exhibit extreme heterogeneity due to different paleogeographic environmental controls and mutual interactions between constructive (e.g., epigenetic paleo-karstification, burial dissolution, structural movement, pressure-solution and dolomitization) and destructive (e.g., physical/chemical compaction, cementation, infilling, recrystallization, and replacement) diagenetic processes. An unconformity-related epigenetic karstification zone was identified in the uppermost fourth member of the Leikoupo Formation, which has developed secondary solution-enhanced pores, vugs, and holes that resulted in higher porosity (1.8–14.2%) and permeability (0.2–7.7 mD). The homogeneity and tightness of the reservoir increases with depth below the unconformity, and it is characterized by primary intergranular and intracrystalline pores, solution pores, fractures, stylolites, and micropores with a lower helium porosity (0.6–4.1%) and permeability (0.003–125.2 mD). Regional seals consist of the Late Triassic Xujiahe Formation, comprised of ~300 m of mudstones that are overlain by ~5,000-m thick of Jurassic to Quaternary continental argillaceous overburden rocks. Effective traps are dominated by a combination of structural-stratigraphic types. Paleo- reservoir crude oil cracking, wet-gases, and dry-gases from three successive hydrocarbon generation processes supplied the sufficient hydrocarbon resources. The homogenization temperatures of the hydrocarbon-associated aqueous fluid inclusions range from 98–130 °C and 130–171 °C, which suggests hydrocarbon charging occurred between 220–170 Ma and 130–90 Ma, respectively. One-dimensional basin evolution models combined with structural geologic and seismic profiles across wells PZ1-XQS1-CK1-XCS1-TS1 show that hydrocarbon migration and entrapment mainly occurred via the unconformity and interconnected fault-fracture networks with migration and charging driven by formation overpressure, abnormal fluid flow pressure, and buoyancy forces during the Indosinian and Yanshanian orogenies, with experiencing additional transformation occurring during the Himalayan orogeny. The predicted estimated reserves reached ~300 × 109 m3. The results provide excellent scientific implications for similar sedimentary basin studies, it is believed that abundant analogous deeply buried marine carbonate hydrocarbon resources yet to be discovered in China and elsewhere worldwide in the near future.