The stability of soil microbial community plays a key role in nutrient cycling, soil organic carbon reservoirs, and plant productivity, making them crucial players in agroecosystems. Although the effect of agricultural intensification on microbial communities has been extensively studied, little is known about the stability of the microbial networks. In this study, we examined the changes in soil properties and the stability of the microbial networks by combining co-occurrence networks and structural equation model under agricultural intensification in Qu Zhou, China. The results showed that agricultural intensification weakened the stability of the bacterial and fungal community networks, the stability of the bacterial network was negatively and positively correlated with the relative abundances of Acidobacteria and Proteobacteria, and, the stability of the fungal network was positively correlated with the relative abundance of Glomeromycota and Basimycota and negatively correlated with Ascomycota. Bacterial and fungal community compositions were correlated with a range of environmental variables including soil organic matter, soil total N, C/N and soil health index (SHI), and SHI, which was the only factors affecting both bacterial network modules. Structural equation modeling combined with correlations between the soil environment and network module suggested that SHI played the most direct role in changes in the microbial phyla and then indirectly stimulated the stability of the microbial networks. Our study highlights the importance of SHI as a comprehensive, key element in shaping the microbial community composition, leading to enhanced microbial network stability.