The southern margin of the Junggar Basin in the Cretaceous-Neogene developed large continental shallow-water lacustrine basins with frequent alternation of dry and wet,cold and warm climate,forming a series of "multicolor" strata,such as gray,grey-green,grey-white,maroon red,red-brown,brick-red,purple-red,and earthy yellow. The study shows that the color of the strata has a good indicator of sedimentary environment. For example,the color index L~*(black and white),a~*(red and green)and b~*(blue and yellow)can clearly distinguish the different subaquatic(semi-deep lacustrine facies,shore-shallow lacustrine facies)or subaerial(river-delta facies,floodplain facies,alluvial fan facies)sedimentary environments. Stratigraphic color evolution sequence can indicate the evolution of Cretaceous-Neogene palaeoclimate. The red sediments can be formed in both the dry and hot land oxidation environment and the relatively reduced underwater environment: "subaerial red",such as brick red sandy mudstone of the Donggou Formation,purple red mudstone of the Ziniquanzi Formation,and maroon to earth red mudstone of the Shawan Formation,40>L~*>52,8>a~*>18,12>b~*>22;"subaquatic red" is characterized by the thick red blocky mudstone of the Hutubihe Formation,35>L~*>45,2.5>a~*>4.5,5>b~*>9. In the Early Cretaceous,the Junggar Basin was relatively warm and humid with wide distribution of lakes. The minimum value of the color index L~*(black and white)was close to 15,and the value of a~* was between -5 and 5,indicating that dark gray to gray dark mudstone was formed in a relatively reducting environment. In the Late Cretaceous,the color index a~* reached the highest peak(15-25),indicating that the climate of the Junggar Basin began to show a trend of drought and heat. During the Eocene to Oligocene,the values of a~* and b~* changed synchronously,and there was an obvious trend of negative drift (7-15),and the climate gradually cooled. In the Neogene,the color index a~* was relatively low(5-9),however,the L~* value was close to 70,indicating that the climate continued to be cool. The research shows that since the end of Cretaceous,the drought-stricken Junggar Basin has been increasingly affected by the global climate cooling and the uplift of Qinghai-Tibet Plateau. The stratigraphic color recorded evolution of paleoenvironment and paleoclimate. Systematic color measurement and analysis can provide an important basis for reconstruction of Mesozoic-Cenozoic sedimentary environment and paleoclimate evolution. It also has a great significance for exploration of global climate change since the Cenozoic.