Based on great number of actual data in the work area, from the aspects of characteristics of coal-seam development, lithologic markers,palaontological assemblage characteristics, etc,the geologic event records of Neogene-Per- mian strata in the southern margin of Junggar Basin were studied deeply. The stratigraphic classification and correlation markers of Neogene-Permian of Chaiwopu Region were established. The geologic event data and the formation of sedimentary cycle are closely related with the ancient climate changes in the Chaiwopu Region, the ancient climate changes affect the changes of sedimentary environment, by which the color changes of sedimentary rocks and lineament of difference of animal-plant combination are induced, for the similarity of these big range of changes,a good marker of stratigraphic classification and correlation is created.