Despite increasing knowledge of plant interactions on the aboveground parts, little is known about the belowground mechanisms underlying such interactions. Here, we selected Picea asperata and Abies faxoniana, two dominant species of subalpine forests, to investigate the effects of planting patterns (isolation and intra- and interspecific interactions) on soil microbial communities. High-throughput 16S rRNA and ITS gene sequencing were performed to explore the bacterial and fungal community structures of the soils. The fungal community changed more under interactions of two species than isolation. Intra- and interspecific interactions had different effects on the fungal community. However, neither intra- nor interspecific interactions had effects on bacterial community composition. Compared with bacteria, fungi were more strongly affected by soil properties, such as the nitrate nitrogen concentration, total nitrogen concentration, pH, and β-1,4-N-acetyl-glucosaminidase activity. These results indicated that fungi were more susceptible than bacteria to plant interactions. Fungal community composition and structure, especially those of ectomycorrhizal fungi, were changed by intra- and interspecific interactions. In inter- and intraspecific interactions with P. asperata, the relative abundance of the ectomycorrhizal fungal Inocybe and Trichophaea increased, which may be one of important factors directly or indirectly affecting belowground interactions.