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The Lower Ordovician Tongzi Formation containing abundant shoal sediments is the most promising stratum for the petroleum exploration in the Sichuan Basin. However, the current studies mainly focus on the central part of the Basin, the systematic analysis of the southeastern part with well-developed shoal facies is lacking. This paper aims to clarify the characteristics and genesis of the Tongzi Formation reservoir in Southeastern Sichuan Basin, following an analysis of sedimentary facies within the sequence stratigraphic framework. The research shows that the main types of reservoir rocks are oolitic, intraclastic and bioclastic dolostones. And the reservoir spaces consist mainly of intergranular (dissolved) pores, intercrystalline (dissolved) pores, intragranular dissolved pores and fractures. Among them, intergranular pores account for the highest proportion, which is followed by intragranular dissolved pores. In addition, most throats are necking and flaky which mainly connect intergranular and intercrystalline pores, respectively. The diagenetic sequence shows that penecontemporaneous karst well improved the porosity of the reservoir in the early-stage although the cementation and compaction reduced parts of pores. The reservoir formation is associated with the tectonic-depositional settings, diageneses and terrigenous contamination. Paleohighlands and submerged uplifts, forming in the early Ordovician amalgamation between Yangtze and Cathaysia blocks, accumulated shoal sediments as the material basis for the reservoir formation. Penecontemporaneous karst forming intragranular dissolved pores and the dolomitization aiding grainstones to resist the pressure solution are the key to increasing porosity and preserving pores. The absence of terrigenous contamination prevented intergranular pores from being strongly cemented, which resulted in the reservoir difference between the central and southeastern Sichuan Basin. The study can be used as a reference for the further exploration of Ordovician petroleum in the Sichuan Basin and other regions owning similar geological settings.