The formation and development of biological soil crusts (biocrusts) potentially affect the cycles and stoichiometric characteristics of soil carbon (C), nitrogen (N), and phosphorus (P). However, it is still unclear how soil microbes adapt to such changes. In this study, we examined the effects of moss-dominated biocrusts coverage (0, 1%-20%, 20%-40%, 40%-60%, 60%-80%, and 80%-100%) on soil physicochemical properties, soil microbial biomass, and ectoenzyme activities [β-1, 4-glucosidase (BG), β-1, 4-N-acetyl glucosidase (NAG), acid phosphatase (AP)] in two soil layers (0-5 and 5-10 cm) in the Three Gorges Reservoir area, as well as the covariations of soil-microbe-ectoenzyme C:N:P stoichiometry. The results showed that biocrust development significantly increased soil clay content, water stable aggregates, soil C, N, P contents, and significantly decreased soil bulk density and sand content. Microbial biomass C, N, P and ectoenzyme activities were significantly increased with increasing biocrust coverage. Soil depth did not affect soil physicochemical properties and C:N:P, but significantly affected microbial biomass, ectoenzyme activities, BG:AP and NAG:AP. Soil C, N and P contents were significantly positively correlated with microbial biomass and ectoenzyme activities, negatively correlated with BG:NAG, while positively correlated with NAG:AP, but had no significant correlation with microbial biomass C:N:P. There was no significant correlation between soil-microbe and microbial-ectoenzyme C:N:P. BG:NAG:AP decreased gradually with the increase of C:N:P stoichiometric imbalance between microbe and soil. This study indicated that the microbial metabolism was co-limited by N and P and with stronger P limitation. Microbes could maintain homeostasis by adjusting their own biomass and ectoenzyme C:N:P to adapt to changes in soil ecological stoichiometry driven by biocrust development.