Abstract: In order to screen microbial agents with good control effects on tobacco root-knot nematodes, microbial agents of Bacillus cereus B3, Bacillus cereus B9 and Bacillus mycoides S2 were applied to tobacco in the fields, and their effects on the bacterial community of tobacco rhizosphere soil and the control of root-knot nematodes were studied by metagenomic sequencing technology. The results showed that the application of Bacillus increased the number of bacteria in the soil, and the number of bacteria in the soil under Bacillus cereus B3 treatment was the highest. Compared to water treatment (CK), Bacillus cereus B3 increased the abundances of beneficial bacteria, such as Nitrospirae, Variovorax and Rhodanobacter. Bacillus cereus B9 increased the abundance of beneficial bacteria Nitrosospira. Bacillus mycoides S2 increased the abundances of Rhodopseudomonas and Mesorhizobium. Pseudomonadaceae was beneficial to the control of root knot nematodes, and its abundance in the soil under Bacillus cereus B3 treatment was significantly higher than that in CK. All of the three microbial agents had a certain control effect against the tobacco disease caused by root-knot nematodes, and the control effect of Bacillus cereus B3 was the best.