Based on the research results of stratigraphic sedimentary facies of Paleogene prototype sedimentary basin in Dabei-Keshen area of Kuqa Depression, the Paleogene Kumglimu Group is divided into five lithologic member, Suweiyi Formation is divided into three lithologic member. It is considered that the sand-conglomerate member of the Kumglimu Group is fan delta deposit, the gypsum-mudstone member is limited lagoon deposit, the dolomite member is limited lagoon-tidal flat deposit, the gypsum salt member is a semi confined lagoon-strong evaporite gypsum salt lake deposit, and the mudstone member is shore-shallow lake deposit. According to sequence stratigraphy and five-level sequence division scheme, the Paleogene prototype sedimentary basin in the central and eastern part of Kuqa Depression is studied, and the entity model of sequence development and evolution is established. It is considered that the prototype sedimentary basin can be divided into two second-level supersequence and three third-level sequence. The Paleogene transgression started from the lower cut valley of rivers in the Dabei-Keshen area. The three third-order sequences are composed of transgressive system tract and highstand system tract cycles, the transition interface between transgressive and highstand system tracts develops the maximum or secondary marine （or lake）-flooding surface.