Hazelnut is one of the four major nuts in the world and has high nutritional and economic value. This study employed Illumina sequencing of ITS rDNA and 16S rRNA genes to identify the seasonal changes in soil microbial community, the predominant environmental factors driving microbial community composition, and the differences in soil microbial composition among different species of the genus Corylus. We found that the soil microbial community composition of species of Corylus changed significantly with the change in seasons. Corylus heterophylla and Corylus kweichowensis had more ectomycorrhiza in their soil compared to Corylus avellane. The main factor influencing fungal community composition in soil was the available potassium, while that of bacteria was the total phosphorus content. Co-occurrence network analysis revealed that the ratio of positive interaction to negative interaction in soil of C. heterophylla and Ping’ou (C. heterophylla × C. avellane) was higher, while the negative interaction of soil community structure in C. avellane was greater. The bacterial community was more stable than the fungal community according to microbial diversity and co-occurrence network analyses. The findings of this research may facilitate improvements to the production and soil system management in hazel planting processes.