Abstract: 【Objective】 To study the characteristics of soil microbial communities under different habitats in Tarim River Basin, and explore the effects of soil environmental factors on soil microbial diversity, so as to provide a scientific basis for studying the important role of microorganisms in the growth and development of Populus euphratica riparia forest. 【Methods】 The soil of Populus euphratica forest in different habitats in the middle reaches of the Tarim River were taken as the research object, the soil microbial community structure and soil physical and chemical properties in 0-100 cm soil layer under three different habitats (arid, mesophilic and periodic flooding) were analyzed. The canonical correspondence analysis and Spearman correlation analysis were used to explore the characteristics of soil microbial community structure and its relationship with soil environment in three different habitats. 【Results】 (1) The soil organic matter, total nitrogen, total potassium, alkali-hydrolyzable nitrogen, available phosphorus and available potassium in mesophilic habitat were significantly higher than those in other habitats (P<0.05); the soil total phosphorus, nitrate nitrogen, ammonium nitrogen and total salt in desert habitat were significantly higher than those in other habitats (P<0.05). (2) There were significant differences in the abundance and diversity of microbial communities in three different habitats. The abundance and diversity of bacteria were the highest in periodic flooding habitat, while the abundance and diversity of fungi were the highest in desert habitat. (3) At the class level of microbial community composition, the dominant bacterial community was γ-Proteobacteria in mesophilic and periodic flooding habitats (relative abundance was 0.20 and 0.29, respectively), while it was Bacillus in desert habitat (relative abundance was 0.31). The dominant fungal community in the periodic flooding habitat was the class Ascomycetes (relative abundance was 0.22), the mesophytic habitat was the class Dictyostelium (relative abundance was 0.30), and the desert habitat was the class Tremella (relative abundance was 0.30). (4) The composition of fungi and bacteria communities in the mesophytic and desert habitats was similar, but the periodic flooding habitat was significantly different from them. (5) The composition of soil microbial communities in the three habitats of P. euphratica riparia was mainly affected by soil total salt, soil water content, available potassium, and nitrate nitrogen. 【Conclusion】 The soil nutrient conditions of P. euphratica riparia in the mesophytic habitat in the middle reaches of the Tahe River are the optimal. The periodic flooding habitat has a richer bacterial microbial community, while the desert habitat has a richer fungal microbial community. The soil environment has a significant effect on the composition of microbial communities.