Soil microbes play a key role in material recycling and energy conversion in arid areas. Currently, research on soil microbial community diversity mainly focuses on environmental change and human disturbance, and not on natural ecosystems. In Xinjiang, a variety of halophytes develop in arid areas, and play an active role in the balance of desert oases ecosystems, but there are relatively few studies on soil microbial community diversity in different halophyte communities. The difference between soil microbial diversity and carbon source utilization under different halophyte communities needs to be elucidated. Therefore, a field experiment was conducted to quantify changes in the functional diversity of the soil microbial community under six halophyte communities (Nitraria tangutorum, Seriphidium kaschgaricum, Karelinia caspia, Bassia dasyphylla, Tamarix ramosissima, and Haloxylon ammodendron) using Biolog analysis in the alluvial fan area of the Manas River watershed. The objective of the present study was to determine 1) the effects of different halophyte communities on carbon source utilization, 2) which halophyte community has stronger activity and microbial functional diversity and 3) the relationship of the ground vegetation diversity and soil microbial community diversity. The results revealed that the average well color development (AWCD) increased with increasing incubation time, and there were significant differences among different vegetation communities, in order of H. ammodendron > K. caspia > N. tangutorum > S. kaschgaricum > T. ramosissima > B. dasyphylla (P < 0.05). There were significant differences among substrates used by soil microbial communities in different halophyte communities (P < 0.05). The substrate used in H. ammodendron was the highest, and that in B. dasyphylla was the lowest. The carbon sources most used by soil microbes were carbohydrates and amino acids, followed by phenolic acids, polymers and carboxylic acids, and the lowest was amines. Principal component analysis (PCA) identified two factors related to carbon sources explaining 4.51% and 25.35% of the variation. Carbohydrates and amino acids were the two main carbon sources separating the two principal component factors. The Shannon and Simpson indices of soil microbial communities in B. dasyphylla were significantly lower than in other communities (P < 0.05), the Pielou index of soil microbial community in N. tangutorum was significantly higher than in other communities (P < 0.05), and there were no significant differences between other communities (P > 0.05). The Margalef, Shannon, and Simpson indices of vegetation communities in S. kaschgaricum, H. ammodendron, and T. ramosissima were more dominant. There were significantly positive correlations between the indices of vegetation richness, diversity, dominance, and soil microbial diversity and dominance (P < 0.05), showing that richer vegetation diversity was related to richer soil microbial diversity. Overall, different halophytic communities have important effects on soil microbial communities in arid areas. The soil microbial community of H. ammodendron has the highest microbial activity and functional diversity.