The soil microbial community structure is critical to the cycling of carbon and nitrogen in forest soils. As afforestation practices increasingly promote different functional traits of tree species, it has become critical to understand how they influence soil microbial community structures, which directly influence soil biogeochemical processes. We used fungi ITS and bacteria 16S rDNA to investigate soil microbial community structures in three monoculture plantations consisting of a non-native evergreen conifer (Pinus sibirica), a native deciduous conifer (Larix gmelinii), and a native deciduous angiosperm (Betula platyphylla) and compared them with two 1:1 mixed-species plantations (P. sibirica and L. gmelinii, P. sibirica and B. platyphylla). The fungal community structure of the conifer–angiosperm mixed plantation was similar to that of the non-native evergreen conifer, and the bacterial community structure was similar to that of the angiosperm monoculture plantation. Fungal communities were strongly related to tree species, but bacterial communities were strongly related to soil nitrogen. The co-occurrence networks were more robust in the mixed plantations, and the microbial structures associated with soil carbon and nitrogen were significantly increased. Our results provide a comparative study of the soil microbial ecology in response to afforestation of species with different functional traits and enhance the understanding of factors controlling the soil microbial community structure.