Pine wilt disease (PWD) caused by the pine wood nematode (Bursaphelenchus xylophilus) is a serious threat to coniferous forests worldwide. However, little is known about how soil microbial diversity responds to PWD and associated management practices. We investigated the community composition and diversity of bacteria and fungi in bulk and rhizosphere soil of Masson pine (Pinus massoniana Lamb.) forests following 0, 1, and 5 year PWD, with the dead pine in a certain plot being either managed (logged and removed from the plot) or unmanaged (maintained as standing dead wood). Both bacterial and fungal alpha diversity decrease after 5 year PWD and logging, with response degree being different between site locations. Alpha diversity of rhizosphere fungi, rather than bacteria, significantly decreases with the disease and logging. We observe an increase in the relative amount of bacterial functional groups involved in carbohydrate and amino acid metabolism after PWD infection and logging practice. With the disease infection, the relative abundance of ectomycorrhizal fungi decreases, while the relative abundance of saprotrophic fungi increases. Compared with logging treatment, unmanaged practice had a weaker effect on soil microbial communities. Our findings provide new insights into the short-term responses of soil microbial diversity to management practices after PWD infection.