Biological soil crusts (biocrusts) fulfill a critical role in ecosystems. However, most research on biocrusts has focused on dryland regions, whereas studies performed in humid regions are limited. Exploring the changes in biocrust systems will enhance our understanding of the role of biocrust in driving ecosystem services and processes of agroecosystem in humid regions. We used microorganisms as indicators and employed the high-throughput sequencing technique to explore the effects of biocrusts on microbial populations (vs. bare soil) in the black soil region of Northeast China. The results indicated that biocrusts increased the percentages of Cyanobacteria, Actinobacteria and Gemmatimonadetes in soil. Additionally, we found that, compared with those in bare soil, biocrusts exhibited more abundant of functional taxa related to cellular-process and metabolism. Moreover, greater diversity (Shannon and Simpson indices) of microbial communities was observed in biocrusts compared with bare soil. Changes in microbial populations of biocrusts resulted in improvements in soil organic matter, total N, total K and available P. These findings are vital for obtaining a greater understanding of biocrust services in humid ecosystems and for conducting more comprehensive assessments of agricultural practices and soil quality in farmlands within the black soil region of Northeast China and other black soil regions worldwide.