The sequence stratigraphy and palaeogeography of the Late Permian Longtan and Changxing formations in Chongqing area of southwestern China have been studied based on the data of outcrops and borehole sections. A total of two third-order sequences are subdivided in the Late Permian; sequence Ⅰ is from the bottom of Longtan Formation to the bottom of C16 coal seam in Longtan Formation, representing a transgressive to regressive cycle; sequence Ⅱ is from the bottom of C16 coal seam in Longtan Formation to the top of Changxing Formation, representing a second regional transgressive to regressive cycle. The favorable coal-forming facies units are mainly the bay-tidal flat facies, followed by residual plain facies, and in the two sequences these facies units controlled coal distribution and they moved towards southwest with a continuous sea-level rise.