Salt is an important environmental factor that affects wheat growth and development and restricts crop production. Bacillus subtilis QM3 is a strain of antagonistic strains which have biological control function. In this paper, the effects of wheat seed, and soaked treatment by B. subtilis QM3, on germination and antioxidant enzyme activities under salt stress were studied. The results showed that under salt stress, B. subtilis QM3 soaking could increase the germination percentage (GP), germination potential (GT), and germination index (GI) of wheat, and significantly increase the activity of catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) (p < 0.05). And high salt concentration had an adverse effect on wheat seed germination. When NaCl concentration were 100, 150, 200 mmol/L, GP, GT, GI decreased to 58.0%, 41%, 61 a/dy, and SOD, POD, CAT decreased to 133.12 gбдmin, 106.62 gбдmin, 6.68 gбдmin. However, the B. subtilis QM3 influenced the variables evaluated. After soaking with B. subtilis QM3, the morphological index GP, GT, GI was significantly increased by 12.99%, 41.18%, and 38.81% at NaCl concentration of 150 mmol/L. Under salt stress (50 mmol/L), B. subtilis QM3 treatment maximized the relative growth rate of CAT activity, which was 87.25%. Similarly, when the NaCl concentration was 150 mol/L, the relative growth rate of SOD activity and POD activity was the greatest, which were 35.81% and 36.57%. It was concluded that B. subtilis QM3 treatment on wheat seeds may be a good option to improve seed germination under salt stress.