Late Permian in Chongqing includes Longtan Formation (Wujiaping Formation) and Changxing Formation, mainly develops transitional facies and shallow marine carbonate facies. Longtan Formation and Wujiaping Formation are contemporaneous, but have different facies. The authors conducted the sequence stratigraphic analysis on Late Permian in this area on the basis of boreholes and outcrop sections. Three sequence boundaries are identified. Two third-order sequences are subdivided in the Upper Permian. In overall, in the third-order sequences of paralic setting, the thickest coal seams tend to be developed in the transgressive system tract.