Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of , leading to more than 50% mortality in field production. In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of for possible microbial antagonists against pathogenic . The microbial diversity and composition were different in the rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the rhizospheric soil from Chongming (Rs_CM) and degenerative rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus ( and ) levels. Correlation analysis of the relative lesion area of corm rot showed that was the most negatively correlated bacterial genus (ρ = -0.7934, < 0.001), whereas was the most negatively correlated fungal genus (ρ = -0.7047, < 0.001). The relative lesion area result showed that from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from rhizosphere soils, and antagonistic activity against pathogenic . was observed on potato dextrose agar medium. corm experiments confirmed that SR38, sp. SR55, SR379, and sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively. This study uncovers the differences in the microbial community of rhizosphere soil of with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.