Volcanism changes the earth's surface building environments where new ecosystems can be constructed. However, the effects of volcanic environmental conditions (e.g. soil moisture, soil organic matter, and available K) on soil microbial communities remains unclear. In the present study, soil samples were collected from two natural habitats (the cone and crater) in Nushan Volcano, China, to investigate the abundances (absolute and relative), compositions, and functions of soil bacterial and fungal communities. The results showed higher 16S rRNA copies, and ITS rRNA copies in the crater compared to the cone. The bacterial and fungal diversities in the crater were higher than in the cone. The soil of the cone and crater displayed distinct bacterial and fungal community compositions based on the nonmetric multidimensional scaling (NMDS). Co-occurrence network analysis revealed the interspecific relationship of soil bacterial and fungal communities was closer in the cone with more links. The number of keystone taxa in the cone was higher than that in the crater. Meanwhile, Nordella and Arthrobacter in bacteria and Stilbella, Tausonia, and Marasmius in fungi were found as the keystone taxa. Moreover, structural equation models (SEM) revealed that soil physicochemical properties had the greatest impact on the composition of bacteria and fungi. Overall, the results advance further research on the effects of microbes on the functions and services of associated ecosystems in extreme environments.