Due to the fact that carbon ion beams irradiation as an important type of ionizing radiation can potentially cause oxidative stress in plants, it is significant to evaluate the antioxidant response of plants to carbon ion beams radiation. Therefore, the objective of this study is to investigate the effects of carbon ion beams irradiation on oxidative stress induced by reactive oxygen species (ROS) and antioxidant response in Arabidopsis thaliana seedlings by irradiating the dry seeds at various doses of carbon ion beams (0, 50, 100, 150 and 200 Gy) and measuring the plant growth parameters, ROS and malondialdehyde (MDA) levels, activities of antioxidant systems and antioxidant-related gene expression. The results showed that 50-Gy carbon ion beam irradiation exhibited stimulatory effects on germination index, root length and fresh weight in Arabidopsis seedlings, while high-dose irradiation (100-200 Gy) inhibited plant growth. Moreover, the production rate of superoxide anion radical, hydroxyl radical generation activity, hydrogen peroxide and MDA contents in Arabidopsis seedlings were obviously increased with the irradiation dose. Additionally, the antioxidant enzyme activities (superoxide dismutase, catalase and peroxidase) and non-enzymatic antioxidant contents (ascorbate and glutathione) in 50-Gy irradiated seedlings were apparently higher than control. Notably, transcriptional analysis displayed that 50-Gy carbon ion beams irradiation could enhance the expression of antioxidant-related genes in Arabidopsis seedlings. These results suggest that the improved activities of antioxidant systems induced by moderate ROS levels play important roles in growth promotion of Arabidopsis seedlings caused by low-dose carbon ion beams irradiation.