From the west to the east across Northeast China, there are three major land use types, ranging from agricultural-pastoral interlaced land, crop land, and forest land. The soil microbial community of each land use type has been reported; however, a thorough comparison of the soil microbial ecology of soils from each land use type has not been made. In the current study, soil samples from agricultural-pastoral land, crop land, and an artificial economic forest were collected from Tongliao, Siping, and Yanji, respectively. The structure and composition of bacterial and fungal communities was investigated by a next generation sequencing protocol, and soil physicochemical properties were also determined. Pair-wise analysis showed some soil parameters were significantly different between agricultural-pastoral land and crop land or forest land, while those soil parameters shared more similarities in crop land and forest land soils. Principal coordinates analysis and dissimilarity analyses jointly indicated that bacterial and fungal communities from each sampling site were quite different. Canonical correspondence analysis and a partial Mantel test showed that the community structures of bacteria and fungi were mainly affected by clay, pH, water soluble organic carbon (WSOC), and total soluble nitrogen (TN). Co-occurrence network analysis and the associated topological features revealed that the network of the bacterial community was more complex than that of the fungal community. Clay, pH, WSOC, and NH4+-N were major drivers and pH and WSOC were major factors in shaping the network of the bacterial community and the fungal community, respectively. In brief, our results indicated that microbial diversity, co-occurrence network patterns, and their shaping factors differed greatly among soils of distinct land use types in Northeast China. Our data also provided insights into the sustainable use of soils under different land use types.