Microorganisms decompose organic substrates to obtain energy. This process releases carbon dioxide (CO2) and is the main cause of soil carbon release in terrestrial ecosystems. Fluctuations in microbial composition significantly affect net CO2 emissions in forests. Because factors are cross-correlated, addressing how they affect soil respiration (Rs), both directly and indirectly, is challenging. In this study, Rs-impacting soil properties, including soil organic carbon (SOC), soil organic nitrogen (SON), microbial diversity (Dsim, indicated by Simpson's diversity index), and total microbial DNA concentration in natural beech forests were examined by structure equation modeling (SEM), which can explicitly evaluate the causal relationships among interacting variables. The results showed that decreasing Dsim, soil temperature, SOC, and SON clearly had direct and indirect effects on Rs under natural conditions. Increasing temperature was a primary factor and promoted a decrease in Rs during the growth season. Dsim was the only parameter with a direct positive effect on Rs, indicating that microbial diversity could accurately predict Rs. Soil nutrient factors indirectly affected Rs through Dsim, which was also affected by soil physical and chemical properties. Significant covariance between SON and Rs (0.42, p < 0.001) indicated multiple interacting variables affecting soil activity. Although the current study suggests that SEM can clarify complex functional processes related to Rs, future studies should consider additional impacting variables such as vegetation properties and enzyme dynamics.