【Objective】The interrelationships within soil microbial communities play a crucial role in maintaining plant health. As an efficient ecological regulation measure for controlling crop soil-borne diseases, the impacts of reductive soil disinfestation (RSD) on the interrelationships of soil microbial communities and its contribution to plant disease control efficacy remain unclear. 【Method】Based on two field experiments, this study systematically investigated the effects of RSD on the intra-kingdom and cross-kingdom interactions within soil bacterial, fungal, and protist communities, as well as the associations between community interactions and tomato growth. 【Result】The results showed that compared with the control, the incidence of tomato bacterial wilt significantly decreased by 90.2% after RSD treatment, while the plant height of surviving plants and tomato yield increased by 13.5% and 57.4%, respectively. RSD treatment significantly reduced the diversity indices of soil bacterial and fungal communities, and significantly altered the community structures of bacteria, fungi, and protists. The microbial groups enriched by RSD treatment included the bacterial phyla Proteobacteria and Acidobacteria, the fungal phyla Ascomycota and Mortierellomycota, and the protist groups Rhizaria and Archaeplastida. Following RSD treatment, the total cohesion within soil bacterial communities, protist communities, and cross-kingdom communities significantly increased. Correlation analysis revealed that compared with community diversity and compositional structure, the total cohesion of bacterial communities, bacteria-fungi communities, and bacteria-fungi-protist communities exhibited stronger and more stable relationships with plant disease incidence, shoot length, and yield, and was significantly negatively correlated with plant disease incidence, and significantly positively correlated with yield and shoot length.【Conclusion】This study highlights the critical role of bacterial and cross-kingdom community interactions in determining plant growth and provides new insights into the disease-suppressive mechanisms of RSD treatment.