ABSTRACTUnraveling how agricultural management practices affect soil biota network complexity and stability and how these changes relate to soil processes and functions is critical for the development of sustainable agriculture. However, our understanding of these knowledge still remains unclear. Here, we explored the effects of soil management intensity on soil biota network complexity, stability, and soil multifunctionality, as well as the relationships among these factors. Four typical land use types representing a gradient of disturbance intensity were selected in calcareous and red soils in southwest China. The four land use types with increasing disturbance intensity included pasture, sugarcane farmland, rice paddy fields, and maize cropland. The network cohesion, the network topological features (e.g., average degree, average clustering coefficient, average path length, network diameter, graph density, and modularity), and the average variation degree were used to evaluate the strength of interactions between species, soil biota network complexity, and the network stability, respectively. The results showed that intensive soil management increased species competition and soil biota network complexity but decreased soil biota network stability. Soil microfauna (e.g., nematode, protozoa, and arthropoda) stabilized the entire soil biota network through top‐down control. Soil biota network stability rather than soil biota network complexity or soil biodiversity predicted the dynamics of soil multifunctionality. Specifically, stable soil communities, in both the entire soil biota network and selected soil organism groups (e.g., archaea, bacteria, fungi, arthropoda, nematode, protozoa, viridiplantae, and viruses), support high soil multifunctionality. In particular, soil microfauna stability had more contributions to soil multifunctionality than the stability of soil microbial communities. This result was further supported by network analysis, which showed that modules 1 and 4 had greater numbers of soil microfauna species and explained more variation of soil multifunctionality. Our study highlights that soil biota network stability should be considered a key factor in improving agricultural sustainability and crop productivity in the context of increasing global agricultural intensification.