Hydrogen peroxide (H2O2) as a widespread molecule plays an important role in plant stress responses. Here, we showed that an Arabidopsis line overexpressing hemoglobin 1 (AtGLB1) can enhance its tolerance to severe hypoxic stress. In our research, Arabidopsis lines with different hemoglobin levels were employed to study the relationship between H2O2 level and the tolerance to hypoxic stress. The relatively low endogenous H2O2 level of AtGLB1-overexpressing plants could be one of the main factors for the increased tolerance of plants to hypoxic stress. Further investigation indicated that the activity of the antioxidant system involved in scavenging H2O2 increased in all three lines examined during hypoxic treatment, while only the line overexpressing AtGLB1 could retain these relatively high levels up to 48 h of the treatment, suggesting that the antioxidant system might play a role in the low H2O2 level of Arabidopsis overexpressing AtGLB1.