Ecosystem degradation is a process during which different ecosystem components interact and affect each other. The microbial community, as a component of the ecosystem whose members often display high reproduction rates, is more readily able to respond to environmental stress at the compositional and functional levels, thus potentially threatening other ecosystem components. However, very little research has been carried out on how microbial community degradation affects other ecosystem components, which hampers the comprehensive understanding of ecosystems as a whole. In this study, we investigated the variation in a soil microbial community through the extinction gradient of an ectomycorrhizal species (Tricholomas matsutake) and explored the relationship between microbial community degradation and ectomycorrhizal species extinction. The result showed that during degradation, the microbial community switched from an interactive state to a stress tolerance state, during which the interactivity of the microbial community decreased, and the reduced community interactions with T.matsutake marginalized it from a large central interactive module to a small peripheral module, eventually leading to its extinction. This study highlights the mechanisms of T.matsutake extinction due to the loss of soil microbial community interactivity, offering valuable information about soil microbial community degradation and the plant ectomycorrhizal species conservation.