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Based on the study of the distribution of intra-platform shoals and the characteristics of dolomite reservoirs in the Middle Permian Qixia Formation in the Gaoshiti–Moxi area of the Sichuan Basin, SW China, the controlling factors of reservoir development were analyzed, and the formation model of “intra-platform shoal thin-layer dolomite reservoir” was established. The Qixia Formation is a regressive cycle from bottom to top, in which the first member (Qi1 Member) develops low-energy open sea microfacies, and the second member (Qi2 Member) evolves into intra-platform shoal and inter-shoal sea with decreases in sea level. The intra-platform shoal is mainly distributed near the top of two secondary shallowing cycles of the Qi2 Member. The most important reservoir rock of the Qixia Formation is thin-layer fractured-vuggy dolomite, followed by vuggy dolomite. The semi-filled saddle dolomite is common in fracture-vug, and intercrystalline pores and residual dissolution pores combined with fractures to form the effective pore-fracture network. Based on the coupling analysis of sedimentary and diagenesis characteristics, the reservoir formation model of “pre-depositional micro-palaeogeomorphology controlling shoal, sedimentary shoal controlling dolomite, penecontemporaneous dolomite benefiting preservation of pores, and late hydrothermal action effectively improving reservoir quality” was systematically established. The “first-order high zone” micro-paleogeomorphology before the deposition of the Qixia Formation controlled the development of large area of intra-platform shoals in Gaoshiti area during the deposition of the Qi2 Member. Shoal facies is the basic condition of early dolomitization, and the distribution range of intra-platform shoal and dolomite reservoir is highly consistent. The grain limestone of shoal facies is transformed by two stages of dolomitization. The penecontemporaneous dolomitization is conducive to the preservation of primary pores and secondary dissolved pores. The burial hydrothermal fluid enters the early dolomite body along the fractures associated with the Emeishan basalt event, makes it recrystallized into medium–coarse crystal dolomite. With the intercrystalline pores and the residual vugs after the hydrothermal dissolution along the fractures, the high-quality intra-platform shoal-type thin-layer dolomite reservoirs are formed. The establishment of this reservoir formation model can provide important theoretical support for the sustainable development of Permian gas reservoirs in the Sichuan Basin.