Excessive Cu2+ is toxic to plants. Carbon quantum dots (CQDs) exhibit certain chelating properties towards heavy metals, and they also demonstrate antioxidant activities. To explore the mechanism for alleviating the Cu2+ toxicity of Salvia miltiorrhiza Bunge mediated by CQDs, CQDs that contained CC, CO, H–O, C–N and C–O functional groups with particle size less than 10 nm and that emitted blue fluorescence were prepared. S. miltiorrhiza seedlings were treated with 200 μM of Cu2+ and 500 mg/L of CQDs to relieve stress. Exogenous CQDs effectively restored plant phenotype; reduced Cu2+, H2O2 and malondialdehyde contents and restored total superoxide dismutase, peroxidase and catalase activities under Cu2+ toxicity. Simultaneously, an association network of Cu2+ transport-related and metabolic pathway genes of phenolic acids and terpenoids was established on the basis of cross-species transcriptome analysis. Combined with reverse transcription quantitative real-time polymerase chain reaction analysis, the potential molecular mechanism of CQDs, i.e. promoting phenolic acid biosynthesis to alleviate Cu2+ toxicity, was revealed by activating the expression of key enzyme genes of phenolic acid synthesis. This study provides a theoretical basis for Cu2+ pollution prevention and control in plants. It also laid a foundation for alleviating Cu stress by using CQDs in agricultural production.