Shelterbelt forests act as a powerful barrier for the safety of the desert highways through preventing wind and fixing sand. In terms of the extremely dry and nutrient-deficient desert soils, the shelterbelt forests along the desert highway highly depend on soil microbes to provide the nutrients for plant growth. This study investigated the microbial communities and enzymatic activities ranging from 0 to 60 cm soil depths in the Tarim Desert Highway shelterbelt forests and the natural desert. Since bacteria and fungi have distinct resource use strategies, the investigation aimed to determine which microbial groups, bacteria or fungi, as well as the habitat-co-observed taxa in both forests and deserts or habitat-specific taxa, were the driving factors of the soil nutrient-cycling functions. Results showed that the bacteria and fungi in the shelterbelt forests had higher species richness compared to those in the deserts (P ＜ 0.01 and P ＜ 0.01, respectively). The community composition of the bacteria and fungi in the shelterbelt forests significantly varied from that in the adjacent natural desert (P ＜ 0.05 and P ＜ 0.01, respectively). Bacteria exhibited a larger increase of 77.5% in terms of species richness compared to fungi's 22.1%, as well as a greater variation of 77% in terms of community composition compared to fungi's 17%. The soil enzymatic activities in the shelterbelt forests were significantly higher than those in the deserts (P ＜ 0.01). The increases in soil enzymatic activity in shelterbelt forests were driven by bacterial community, rather than environmental factors or the fungal community. The partial Mantel test demonstrated that there is a significant correlation between soil enzymatic activities and both the species richness and community composition of bacteria (rho=0.46, P ＜ 0.01 and rho=0.68, P ＜ 0.01, respectively). When other variables were controlled for, the abundance of habitat-co-observed bacteria and the species richness of habitat-specific bacteria (rho=0.47, P ＜ 0.01 and rho=0.36, P ＜ 0.01, respectively) were significantly correlated with soil enzymatic activities in the shelterbelt forests and deserts. This suggests that habitat-co-observed bacteria and habitat-specific bacteria play different roles in regulating soil enzymatic activities. The findings of this investigation indicate that soil bacteria prevail over soil fungi in reacting to the construction of the desert highway shelterbelt and that soil bacteria can enhance soil microbial functions through alternations to the abundance of local bacterial species and the influx of non-local bacterial species.