To investigate the effects of high-temperature flame treatment on soil microbial community structure and to clarify the impact of soil thermal disinfection technology on soil organisms, this study established two treatments: a high-temperature flame treatment (T) and a traditional control (CK). Soil samples were collected immediately after the treatment and following a short-term recovery period. Combining high-throughput sequencing with soil nutrient analysis, the effects of the treatment on soil microbial community structure and soil fertility were evaluated. Immediately following the high-temperature treatment, the contents of soil available nitrogen (AN) and available potassium (AK) significantly increased by 8.29% and 23.09%, respectively, whereas soil pH, organic matter (OM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), and available phosphorus (AP) exhibited no significant changes. Bacterial alpha diversity indices (Chao, Sobs, ACE, and Shannon) decreased significantly, indicating reduced community richness and diversity. Principal component analysis (PCA) revealed a distinct separation in community structure between treatments, with a significant decrease in beta diversity. The relative abundances of Chloroflexi and Acidobacteriota decreased by 4.08% and 2.29%, respectively, whereas those of Pseudomonadota, Bacteroidota, and Actinobacteriota increased by 0.80%, 2.00%, and 1.45%, respectively. The species abundances of the top ten dominant genera underwent significant changes, indicating a substantial alteration in the bacterial community structure. After a short-term recovery, bacterial alpha diversity indices showed no significant differences compared to the control, and community richness basically recovered to the control level. PCA revealed no distinct separation between treatments, indicating that the overall microbial community structure recovered to a level similar to the control. The relative abundances of Actinobacteriota and Bacillota increased by 1.15% and 0.40%, respectively, while Acidobacteriota decreased by 0.59%, with minor differences observed in other dominant phyla. Furthermore, compared to pre-treatment levels, the relative abundances of Chloroflexi and Acidobacteriota both decreased by 18.2%, Pseudomonadota increased by 12.8%, and Actinobacteriota surged by 122.6%, with no significant difference observed in Bacteroidota. Correlation analysis indicated that changes in soil nutrients might be an important driving factor for the differences in the recovered microbial community structure. This study reveals the disturbance and short-term recovery effects of high-temperature flame treatment on soil nutrients and microbial communities. In the short term, the treatment significantly reduced bacterial community diversity and richness. Following short-term recovery, community diversity and overall structure were rebuilt, although the community composition experienced continuous succession, demonstrating that the soil microbial community possesses the potential for rapid diversity recovery. These findings suggest that this technology does not cause persistent adverse effects on soil organisms, providing a basis for its environmental safety and application potential.