Paleokarst is a major contributory factor for natural gas reservoir development of the Middle Permian Maokou Formation in Sichuan Basin, South China. To promote the reliability of the paleokarst geomorphology estimations, which are fundamental for the prediction of paleokarst reservoir distribution, a process combining sequence stratigraphic correlation, paleokarst genesis analysis, paleogeographic reconstruction and sequence stratigraphic thickness variation studies is implemented. Three 3rd-order sequences (named TR1–TR3) are defined in the Maokou Formation based on the literature and the carbonate δ13C chemostratigraphy, according to which 147 boreholes and outcrops are correlated via lithology, well log and seismic data. The results of sequence stratigraphic correlation reveal that thickness variations of TR3 stratigraphy are complicated and heterogenous, including three areas of abnormally thinned strata: southern Sichuan Basin, northern Sichuan Basin and Chengdu region. However, along with the paleokarst and paleogeographic studies, only the stratigraphic thinning of southern Sichuan Basin is related to subaerial exposure and karstification, whereas that of northern Sichuan Basin and Chengdu region are due to sedimentary differentiation. Consequently, the paleokarst geomorphology of Maokou Formation is estimated from stratigraphic thickness combined with sedimentary factors. The paleohigh located at the Luzhou region in southern Sichuan Basin, where the TR3 stratigraphy is absent. Around the peleohigh, most of the basin acted as karst slope and karst basin with gentle gradients. Meanwhile, the northern part of basin shows little evidence of paleokarst inside the Maokou Formation, appearing to be continuous sedimentary platform. The paleogeomorphology pattern is consistent with the discovered distribution of Maokou paleokarst reservoir and can be utilized in play evaluation.