In contrast to the widely used sequence stratigraphic models for passive continental margins, the stacking patterns of strata within epeiric seas, which are influenced by regional tectonic activity, may display opposing characteristics during the same geological period. These variations serve as a record of basin evolution and also affect the accumulation of hydrocarbons within the strata. Our study investigated the development potential of the deep Longmaxi Shale in the southern Sichuan Basin by examining the sequence stratigraphy and sedimentary fill patterns. Using a combination of core observation, well-logging data analysis, and 3D seismic profile interpretation, we aimed to gain an understanding of the sedimentary fill history of the Longmaxi Shale during the Early Silurian. Our analysis revealed that deglaciation and regional tectonic events affected the sequence stratigraphy, resulting in unconformities that were identifiable using seismic data and wireline logs. Through an analysis of thirty wireline logs and two seismic profiles, we identified two third-order sequences suggested in the Lower Longmaxi Formation. Within the two third-order sequences were five systems tracts, with the first exhibiting a complete cycle of sea-level change and the second cycle being incomplete due to regional tectonic events. The graptolite succession on the upper Yangtze Platform provided a temporal view of the sequence stratigraphy and sedimentation rates of the Longmaxi Shale. The thickness trends of the systems tracts reflected the interplay of short-term eustasy fluctuations, subsidence, and uplift. Our analysis suggests that regional subsidence played a significant role in the deposition of the second transgressive systems tract (TST) in the Weiyuan and Luzhou areas, which represents a promising target for shale gas exploration, in addition to the first TST. However, the Changning area experienced a relative sea-level decrease due to the intense uplift of the Qianzhogn Paleo-uplift and the increased supply of sediment and is interpreted as a highstand systems tract (HST); it is not considered to have shale gas exploration potential.