Limited data are available on the molecular and physiological mechanisms for increased pH-mediated amelioration of copper (Cu) toxicity in plants. Citrus sinensis seedlings were fertilized with a nutrient solution at the Cu concentration of 300 (Cu toxicity) or 0.5 mu M (control) and a pH of 3.0, 4.0, or 4.8 for 17 weeks. Subsequently, we examined the interactive effects of low pH and Cu toxicity on transcriptomics, metabolomics, and some physiological parameters in leaves. Our results demonstrated that increased pH reduced Cu toxicity-induced leaf Cu accumulation and oxidative damage by reducing reactive oxygen species (ROS) production and maintaining the homeostasis of sulfur (S)-containing compounds (reduced glutathione), ascorbate, and cell redox potential, thus mitigating Cu toxic effects on leaf chlorophyll biosynthesis, photosynthesis, and metabolisms of carbohydrates, lipids, amino acids, and secondary metabolites. The increased pH mitigated Cu toxicity-induced impairment of cell wall metabolism by reducing cell wall Cu concentration, thus improving leaf growth. Under low pH (pH 3.0), C. sinensis leaves also displayed some adaptive responses to Cu toxicity to meet the increased demand for the dissipation of excess light energy and the detoxification of Cu and ROS, including: (a) increased distribution of Cu in cell wall; (b) elevated photorespiration and thermal dissipation; (c) increased accumulation of nonstructural carbohydrates [fructose, glucose, starch, total nonstructural carbohydrates (the summation of fructose + glucose + sucrose + starch), maltotetraose and 1,1-kestotetraose] and upregulation of metabolism (glycolysis/ gluconeogenesis, pyruvate metabolism and pentose phosphate pathway) related to energy production; (d) downregulation of phospholipid [LysoPC 18:3(2 n isomer)] and phosphate-containing compounds (2 '-deoxycytidine-5 '-monophosphate and adenosine 5 '-monophosphate) and upregulation of L-tryptophan metabolism and related amino acids (L-tryptophan and 5-hydroxy-L-tryptophan); and (e) increased accumulation of some secondary metabolites [total phenolics, lignin, alkaloids (3-indoleacrylic acid, N-acetyl-5-hydroxytryptamine and methyl nicotinate), plumerane (indole and 3-indolepropionic acid) and coumarins (isoscopoletin, scopoletin, skimming and scopolin)]. However, these adaptive responses could not protect low pH-treated leaves from Cu toxicity, as indicated by elevated malondialdehyde accumulation and electrolyte leakage and decreased photosynthesis and chlorophyll level in leaves as well as reduced leaf growth due to impaired cell metabolism. Cu toxicity intensified the adverse effects of low pH on C. sinensis leaves.