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Microwave irradiation is a new means of non-toxic, residue-free, and green soil disinfection that prevents and controls soil diseases, insects, and weeds and helps to improve crop quality and yield. Soil microorganisms, as an important part of the ecosystem, are closely related to crop growth and health. To investigate the changes of soil physicochemical properties and microbial communities during microwave soil disinfection for different time periods, phaeozems from northeastern China were selected for microwave treatment at 3, 6, 9, and 12 min, and their physicochemical properties were measured after 30 days of incubation. The test soils (0–20 cm) after 30 days of incubation were used, and high-throughput sequencing was performed to detect changes in their soil microbial structure under different microwave time treatments. Microwave treatment had significant effects on soil pH, nitrate (NO3--N), ammonium (NH4+-N), and available phosphorus (AP) content. As shown by the Shannon, Chao, and Ace indices, microwave treatment at 3 min had the lowest effect on bacterial diversity compared to the control treatment (CK). Shannon index decreased by 9.92%, 24.56%, 34.37%, and 38.43% after 3, 6, 9, and 12 min microwave treatments, respectively; Chao index decreased by 7.69%, 18.13%, 32.21%, and 57.91%, respectively; Ace index decreased by 6.40%, 6.98%, 20.89%, and 52.07%, respectively. The relative abundance of beneficial soil microorganisms Micromonospora, Fictibacillus, Paenibacillus, and Bacillus (Firmicutes) increased significantly compared to CK. The results indicated that although the microwave treatment altered the soil microbial community, beneficial soil microorganisms showed faster recovery. In addition, pH, soil organic carbon (SOC), total nitrogen ratio (C/N), soil-available phosphorus (AP), and NO3--N were important factors affecting bacterial community diversity and composition following microwave treatment, and bacterial community composition was driven by soil chemical properties such as soil pH, SOC, C/N, and NO3--N. Microwave treatments at different time periods affected soil microbial community structure to different degrees, and soil bacteria of copiotrophic taxa (e.g., Firmicutes) were relatively higher than the control. Overall, microwave treatment from 3–6 min may be more suitable for soil disinfection. The study of the effect of microwave on soil physicochemical properties and bacterial microbial community not only provides some scientific reference for the rational application of microwave soil disinfection, but also has positive significance for soil-borne disease control and crop quality improvement. [ABSTRACT FROM AUTHOR]