In this study, we examined the possible mechanisms of trehalose (Tre) in improving copper-stress (Cu-stress) tolerance in rice seedlings. Our findings indicated that pretreatment of rice seedlings with Tre enhanced the endogenous Tre level and significantly mitigated the toxic effects of excessive Cu on photosynthesis- and plant growth-related parameters. The improved tolerance induced by Tre could be attributed to its ability to reduce Cu uptake and decrease Cu-induced oxidative damage by lowering the accumulation of reactive oxygen species (ROS) and malondialdehyde in Cu-stressed plants. Tre counteracted the Cu-induced increase in proline and glutathione content, but significantly improved ascorbic acid content and redox status. The activities of major antioxidant enzymes were largely stimulated by Tre pretreatment in rice plants exposed to excessive Cu. Additionally, increased activities of glyoxalases I and II correlated with reduced levels of methylglyoxal in Tre-pretreated Cu-stressed rice plants. These results indicate that modifying the endogenous Tre content by Tre pretreatment improved Cu tolerance in rice plants by inhibiting Cu uptake and regulating the antioxidant and glyoxalase systems, and thereby demonstrated the important role of Tre in mitigating heavy metal toxicity. Our findings provide a solid foundation for developing metal toxicity-tolerant crops by genetic engineering of Tre biosynthesis.