The potted seedlings of Malus baccata were used as materials in the treatments of simulated suboptimal rootzone temperature（5 ℃） in culture room. The treatments included the suboptimal rootzone temperature (L), L + exogenous GABA (LG) and L + VGB (LV), the white roots were cut at 0, 12, 24, 48, 96, and 144 h after treatment, respectively. We measured the contents of endogenous GABA, osmotic adjustment substances and reactive oxygen species, the activities of antioxidant enzymes to investigate the regulating effect of GABA on the antioxidant system in roots under suboptimal rootzone temperature. The results showed that: (1) the endogenous GABA content in the roots of Malus baccata increased under the L treatment, osmotic adjustment substances accumulated in different degrees. And as a consequence, the contents of superoxide anion (O₂^-·) and hydrogen peroxide (H₂O₂) increased significantly. The peroxidation in roots was deepened. (2) Exogenous GABA increased the contents of endogenous GABA in roots, soluble sugar, soluble protein and proline (Pro) in the roots, significantly enhanced the activities of superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) in roots, and effectively reduced the contents of H₂O₂ and O₂^-·, which meant exogenous GABA could significantly alleviate the degree of membrane lipid peroxidation. (3) The effect of VGB, which is the specific inhibitor of GABA (LV), treatment was opposite to that of LG treatment. Those results indicated that the GABA metabolism had a positive effect on the defense of the roots to the oxidative stress triggered by suboptimal rootzone temperature, and exogenous GABA had the effect of enhancing the antioxidant capacity of the roots through regulating endogenous GABA metabolism.