BACKGROUND: The soybean cyst nematode (SCN, Heterodera glycines) is the most devastating and yield-limiting pest in soybean worldwide. With the increasing awareness of environmental protection, biological control becomes more and more urgent. The Bacillus megaterium Sneb207 has previously shown the ability to inhibit the movement of SCN, but little is known about its effect on nematode control in agricultural settings. The aim of this study was to evaluate the efficiency of Sneb207 against SCN and investigate the ability of Sneb207 to induce systemic resistance to H. glycines in soybean. RESULTS: The stability and efficiency of SCN control by Sneb207 was assessed in two field experiments. Compared to nontreated control, Sneb207 significantly reduced the number of cysts, SCN juveniles, and eggs, while it promoted soybean growth. Furthermore, results of two pot experiments showed that the number of initial infections of second-stage juveniles were 231.75 and 131.3 after Sneb207 treatment, respectively, lower than control (274.75 and 215.33). Sneb207 reduced the total number of juveniles and females, and lengthened SCN development time. Moreover, through the split-root system and real-time quantitative PCR experiments, we found that Sneb207 induced systemic resistance and enhanced the gene expression of GmACS9b, GmEDS1, GmPAD4, GmSAMT1, and GmNPR1-1 involved in the salicylic acid, jasmonic acid and ethylene pathways at different levels. CONCLUSION: Our results demonstrate that B. megaterium Sneb207 inhibits the invasion, the development, and reproduction of SCN by inducing systemic resistance. The overall outcomes of the present study support B. megaterium Sneb207 as a potential biocontrol agent for H. glycines.