In order to solve the problems of soil continuous cropping obstacle and microbial community imbalance caused by long-term intensive planting in facility agriculture in China, the concept of biological soil disinfestation (BSD) was introduced in this study. Biogas slurry was used as exogenous carbon source and inoculum to induce in-situ anaerobic fermentation of soil, five treatments were set up, including control (CK), single flooding control (WCK), low (LG), medium (MG) and high (HG) biogas slurry concentrations, in-situ anaerobic fermentation was carried out at 37 ℃ for 15 days, and the effects of biogas slurry-driven BSD process on soil physicochemical properties and microbial community evolution were explored. The results showed that compared with CK and WCK, biogas slurry fermentation significantly increased soil pH and effectively alleviated soil acidification. Available potassium and phosphorus contents increased significantly, while organic matter and total nitrogen contents decreased significantly due to fermentation consumption, and organic matter content was lower under biogas slurry fermentation than under WCK. Microbial diversity analysis showed that the bacterial Chao1 index in biogas slurry fermentation treatments was higher than those in the CK and WCK, and LG and MG maintained higher bacterial diversity, while WCK stimulated the growth of fungi. PCoA and LEfSe analyses demonstrated that biogas slurry fermentation reconstructed the soil microbial community structure, and the community structures of the LG and MG treatments were similar. At the functional level, MG and HG treatments up-regulated the relative abundance of functions such as cofactor and vitamin metabolism, while biogas slurry fermentation generally reduced carbohydrate metabolism functions. Functional mining using the NCyc and PCyc databases revealed that biogas slurry fermentation significantly altered the abundance distribution of functional genes involved in nitrogen and phosphorus cycling. It generally increased the relative abundance of key functional genes such as nmo, nosZ, and gdh_K00262, synergistically enhancing mineralization, denitrification, and ammonia assimilation processes. This improved the microbial capacity to utilize organic energy substances in the biogas slurry while simultaneously mitigating the risk of N₂O emissions. Specifically, the MG treatment exhibited a relatively balanced enhancement across various functional genes. In conclusion, the 15-day in-situ anaerobic fermentation driven by biogas slurry activated soil microbial metabolism by triggering a strong positive excitation effect, drove the steady-state succession of the community to the direction of eutrophic obligate anaerobic, and significantly improved the bioremediation efficiency and nutrient supply capacity of facility degraded soil. Among them, MG combined with in-situ anaerobic fermentation had the best effect in improving soil properties and reconstructing microbial community function. This study proved the feasibility of biogas slurry as BSD additive to repair facility soil, and provided a theoretical basis for the resource utilization of biogas slurry and the treatment of continuous cropping obstacles.