Soil salinization is serious in the arid and semi-arid region in the northwest of China, especially in Xinjiang. In this paper, soil samples with different salt contents were collected in Junggar Basin and Tarim Basin of Xinjiang. X-ray diffraction (XRD), transmission electron microscopy (TEM) and X-ray fluorescence (XRF) were employed to investigate the formation and distribution characteristics of clay minerals in salinized soil profiles. In these two basins, salinized soils with different salt contents had similar mineral composition including illite, montmorillonite, chlorite and kaolinite. In Tarim basin, illite is the main clay mineral while montmorillonite was bare. The analysis results of the δ¹³C and δ¹⁸O values in secondary carbonate and the D and δ¹⁸O values in clay minerals reflected that C4 plants were the dominant plant and the climate was relatively dry during the formation of salinized soils in Tarim Basin. The arid climate in Tarim Basin is unconducive for depriving K⁺ from illite, the content of montmorillonite reached the lowest point. The content of montmorillonite in salinized soils in Junggar Basin is significantly negatively correlated with the content of illite, (r=0.81, n=30, P<0.01). More specifically, this phenomenon demonstrates that illite in salinized soils was transformed to montmorillonite. In generally, this transformation is affected by water condition and requires the deprivation of K⁺ and Al³⁺, entry of Si⁴⁺, and replacement of K⁺ by Ca²⁺ and Na⁺ within lattice layers. According to the analysis, salinized soils in Junggar Basin have the required moist condition and chemical components to transform illite to montmorillonite: 1) Under the relative humid condition, K⁺ of illite in soil would be easily leached; 2) pH of salinized soil is high (pH＞8.5), which promotes Si4+ of primary mineral to be readily dissolved. 3) Large amounts of Ca²⁺, Na⁺ and Mg²⁺ in soil solution of salinized soils. Thus, the content of montmorillonite in salinized soils in Junggar Basin is more than that in Tarim Basin. There is a significant negative correlation (r=0.76, n=22, P<0.01) between the contents of illite and salt in soil layers deeper than 10 cm, which indicates that soil layers below 10 cm depth are moister, the existed salts promote the transform of illite to montmorillonite in Junggar Basin. Thus, climate condition and salt content in salinized soils are the main factors for the formation and transformation of clay minerals in Junggar Basin and Tarim Basin of Xinjiang.