Biological crusts play a significant role in influencing the physical and chemical characteristics of soil, as well as in shaping microbial diversity. Nevertheless, there remains a notable deficiency in research regarding the impact of biological soil crust development on the underlying soil within inland saline-alkali wetland ecosystems. This study examined soil physicochemical properties and enzyme activities before and after crust formation and crust layers in the Longfeng Wetland of Daqing City, Heilongjiang Province. High-throughput sequencing and RDA were used to analyze bacterial and fungal abundance, community structure, and environmental factors. The study identified drivers of microbial community composition and employed PICRUSt and FUNguild to predict the potential functions of dominant species. Results showed that subsurface soil salinity decreased after crust development. Subsurface soil organic carbon, total phosphorus, organic phosphorus, and available potassium contents, along with sucrase, urease, alkaline phosphatase, and catalase activities, were significantly elevated. The proportions of sand and silt also increased, indicating that biocrust growth can enhance nutrient enrichment and ameliorate soil texture. The analysis of microbial diversity reveals that crust development significantly influences the formation of dominant species within both bacterial and fungal communities beneath these crusts. Notably, bacterial community diversity is substantially higher than fungal community diversity. The abundances of dominant bacteria and fungi in crust layers and subsurface soils were significantly higher than in bare soil. At the phylum level, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant bacterial groups, while Ascomycota and Basidiomycota dominated fungal communities. At the genus level, the dominant bacteria were Anditalea, Egicoccus, and Mongoliibacter, while the dominant fungi were Verticillium, Neocamarosporium, and Fusarium. The weighted path of the structural model was used to explore correlations among soil salinity, enzyme activity, nutrients, and microbial richness. The model-fitting results indicated that soil nutrients strongly influenced microbial richness. Among them, available potassium, alkali hydrolyzable nitrogen, organic carbon, salinity, and pH are the important factors that can significantly affect the composition of microbial communities. We also found that endophyte-lichen parasite-plant pathogen-undefined saprotroph was the most abundant in fungal function. Bacterial functions were predominantly annotated to metabolic processes, with the most prominent pathways including amino acid metabolism, carbohydrate metabolism, and the metabolism of cofactors and vitamins, all exhibiting relatively higher abundances. The increased bacterial abundance effectively enhanced soil nutrient content and facilitated the restoration of desertified soils. In conclusion, these findings provide an important microbiological theoretical basis for analyzing the restoration effect of biological soil crust development on urban wetland ecology.