Abstract: Late Permian in Chongqing includes Longtan Formation (Wujiaping Formation) and Changxing Formation, mainly develops transitional facies(bay milieu(lagoon deposit)—tidal flat facies) and shallow marine carbonate facies. Longtan Formation and Wujiaping Formation are contemporaneous, but have different facies. We have conducted the sequence stratigraphic analysis on Late Permian in this area on the basis of boreholes and outcrop sections. Three sequence boundaries are identified which are represented by regional tectonic unconformities at the bottom of the Upper Permian, sedimentary facies reversal surface at the base of the No.16 coal in the Longtan Formation, and the event stratigraphic boundary at the top of the Upper Permian. Two third-order sequences are subdivided in the Upper Permian. Because the study area is located in the paralic basin, the thick coals tend to be developed near the transgressive surface. In overall, in the third-order sequences of paralic setting, the thickest coal seams tend to be developed in the transgressive system tract.