The soil fungal community plays an important role in maintaining soil ecosystem functions in arid areas. In this study, we collected soil samples (i.e., within the canopy, at the edge of the canopy, and at the edges of shrubs) from nebkhas and non-nebkhas Tamarix shrub communities at the Yingsu section of the lower reaches of Tarim River, Xinjiang, China. High-throughput sequencing technology was used to explore the composition and structure of the soil fungal community in these samples; the distribution of soil fungal communities in nebkhas and non-nebkhas Tamarix shrubs, as well as the comprehensive effects of nebkhas and soil factors on soil fungal communities and functions, was also determined. The following results were obtained. (1) Soil pH, available K, total K, ammonium N, and available P significantly differed according to the location of the Tamarix shrubs, but no significant differences in soil moisture, electrical conductivity, total salt, organic matter, total N, total P, and nitrate N in whole shrubs were noted. (2) The soil fungal community structure of nebkhas and non-nebkhas Tamarix shrubs showed some similarities. The soil fungi of Tamarix shrubs could be divided into 1 kingdom, 14 phyla, 48 classes, 110 orders, 227 families, 410 genera, and 557 species. Species from the phyla Ascomycota, Basidiomycota, and Mortierellomycota and the genera Alternaria, Aspergillus, Stolonocarpus, Colletotrichum, Unidentified_saccharomycetales_sp, and Gymnoascus clearly dominated the fungal communities observed. (3) db-RDA showed that total N, available K, and ammonium N are the main environmental factors affecting the structure of the soil fungal communities. Spearman correlation analysis showed significant positive correlations between total P and Aspergillus, Microthelia, Gymnoascus, and Phialosimplex and between total N and Alternaria. (4) Function prediction using FUNGuild revealed three types of saprotrophic, symbiotrophic, and pathotrophic functional bacteria and five types of cross-trophic functional fungi in the Tamarix shrubs. Saprotrophic functional fungi dominated (30.0%) other types of fungi in these shrubs. (5) Although the enrichment effect of the nebkhas and canopy of Tamarix shrubs had no obvious effects on soil nutrients and microorganisms, significant differences in the functions of the fungi were observed. The comprehensive effect of the nebkhas and canopy of Tamarix shrubs also indicated a great impact on the functional composition of soil fungi.