By making full use of the core and logging data of more than 40 exploration wells, this paper divides the sequence stratigraphy of the Permian Maokou Formation in eastern Sichuan Basin, analyzes the characteristics of the sequence boundary, establishes the isochronous sequence stratigraphic framework, summarizes the stratigraphic filling law, and discusses the sedimentary-paleogeographic pattern and the distribution of favorable reservoir areas in the sequence framework. Three type I sequence boundaries and three type II sequence boundaries of Maokou Formation are identified, and a new scheme for dividing Maokou Formation into five third-order sequences is proposed. The sequence stratigraphy of Maokou Formation generally has the characteristics of bottom overlap and top erosion. The bottom of SQ1 overlap from northeast to southwest towards Hercynian paleouplift and paleogeomorphic highland, and the top of SQ5 is missing in varying degrees due to the Dongwu movement. Generally, the strata in the sequence framework show the distribution trend of east-west differentiation and alternating thickness: a banded stratigraphic thickening zone is developed in the middle of the study area for SQ3 and SQ4 sequences, which probably correspond to shoal belt of the weakly bordered platform margin. To the east of this zone is the stratigraphic thinning area, which is consistent with the deep-water sedimentary area where mudstone, shale and siliceous shale are developed in Gufeng section. It shows the paleogeographic pattern of gradually deepening from west to east and from carbonate platform to shelf. It is pointed out that the superposition of favorable reservoir facies belt in sequence stratigraphic framework and early diagenetic karst transformation under type I sequence boundary is conducive to the formation of characteristic karst limestone reservoir in Maokou Formation.