This paper uses various data such as well logs and drilling records to study the characteristics of palaeo-biota fossil combination and clay minerals from the variegated mudstone in the Shinan area of the Junggar basin, and analyses their lithologic and electric properties. Based on age contrast of spores and pollens and analysis of clay minerals, it was proved that the variegated mudstone is a regional weathering crust. The study ascertained the boundary of the Cretaceous and the Jurassic and the initial sedimentary age of the variegated mudstone: The results show that the weathering crust exhibits planar zonation and vertical stepwise structure. Every unit has clear diagnostic log response. The variegated mudstone belongs to the Jurassic Xishanyao Formation and the Toutunhe Formation is generally absent in the Shinan area. The Cretaceous Qingshuihe Formation overlaps the variegated mudstone, while the Jurassic Xishanyao Formation is truncated by the variegated mudstone. The authors hereby made new boundaries between the Cretaceous and Jurassic, the Jurassic Toutunhe and Xishanyao Formations, and proposed a new division scheme.