The Lower Silurian Shiniulan Formation in southern Sichuan is a key emerging target for marine carbonate hydrocarbon exploration in the Sichuan Basin. However, insufficient understanding of its sedimentary environments and reef-shoal evolution greatly hinders Silurian carbonate exploration and recognition of basin-wide Silurian paleogeography and filling processes. Based on field outcrop profiles, drilling and well-logging data, seismic attributes and core thin-section observations, this study carries out high-resolution stratigraphic cyclic division, fine sedimentary facies analysis and reef-shoal spatial-temporal mapping to systematically reveal the evolution and controlling factors of multi-stage carbonate reef-shoal complexes. Three main conclusions are drawn: (1) Four carbonate sedimentary cycles are recognized in the Shiniulan Formation, corresponding in ascending stratigraphic order to the Lower Submember 1, the Upper Submember 1, the Lower Submember 2, and the Upper Submember 2. (2) Carbonate ramp and platform depositional systems dominate the formation, consisting of inner ramp, middle-outer ramp, open platform, platform margin and platform marginal slope facies, while the coeval eastern Xiaoheba Formation develops delta-shelf clastic sequences. (3) Each cycle contains three major limestone zones distributed in the northern, central and southern parts of the study area. Extensive reef-shoal bodies mainly occur in the Upper Submember 1 and the Lower Submember 2 and are predominantly controlled by paleotopographic highs. Regional relative sea level evolved from gradual shallowing to subsequent deepening; the Upper Submember 1 recorded the lowest relative sea level, the most restricted marine extent, and the broadest reef-shoal distribution, representing a promising hydrocarbon exploration play. This study provides theoretical support and geological basis for reservoir prediction and favorable play optimization of Silurian carbonates across the Sichuan Basin.