Drought stress is widespread worldwide, which severely restricts world food production. The antioxidant property of carbon dots (CDs) is promising for inflammation and disease treatment. However, little is known about the functions of CDs in the abiotic stress of plants, especially in drought-resistant fields. In this study, CDs were synthesized using cysteine and glucose by the hydrothermal method. The in vitro antioxidant capacity of CDs and the reactive oxygen species (ROS) scavenging capacity were evaluated. We speculate on the antioxidant mechanism of CDs by comparing size distribution, fluorescence spectra, elements, and surface functional groups of CDs before and after oxidation. Besides, we evaluated the effects of CDs on seed germination and seedling physiology under drought stress. Also, the responses of antioxidant CDs to long-term drought stress and subsequent recovery metabolism in tomato plants were evaluated. The results show that CDs accelerated the germination rate and the germination drought resistance index by promoting the water absorption of seeds. CDs enhanced the drought resistance of seedlings by improving the activity of peroxidase (POD) and superoxide dismutase (SOD). Moreover, CDs can activate the antioxidant metabolism activity and upregulate the expression of aquaporin (AQP) genes SlPIP2;7, SlPIP2;12, and SlPIP1;7. All of these results render tomato plants distinguished resilience once rewatering after drought stress. These results facilitate us to design and fabricate CDs to meet the challenge of abiotic stress in food production.