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• No negative effects occurred for SAR (pH 3.5 and pH 4.5). • SAR (pH 2.5) reduced chloroplasts and damaged the outer leaf layers. • SAR (pH 2.5) altered genes related to photosynthesis and various metabolic pathways. • Plants respond to SAR stress by mechanisms of resistance, avoidance, and escape. Tea plants (Camellia sinensis (L.) O. Kuntze), which are typically cultivated in high-elevation mountainous regions in southern China, are severely affected by acid rain. Our recent study indicated that simulated acid rain (SAR) at pH 2.5 produced necrotic spots on the leaf surface, impaired plant development by inhibiting photosynthesis and the antioxidant defense system, and caused metabolic disorders. In contrast, a pH of 4.5 had no toxic effects on tea seedlings. However, molecular-level evidence for these conclusions is still lacking. In this study, we explored the changes in leaf micromorphology under different SAR treatments using electron microscopy, and presented the first case study on the systemic responses of the tea leaf transcriptome to SAR. An examination of leaves using transmission electron microscopy (TEM) and scanning electron microscopy (SEM) showed that SAR (pH 4.5 and pH 3.5) did not impair the epidermis or chloroplast structures, but SAR (pH 2.5) reduced the number of chloroplasts, corroded epicuticular wax and trichomes, and altered stomatal density and size. Transcriptomic analysis revealed that the expression of multiple genes related to photosynthesis and carbohydrate, nitrogen, and sulfur metabolism were altered under SAR. Additionally, epicuticle wax biosynthesis and plant hormone signal transduction pathways were found to significantly influenced by high-acidity SAR. Taken together, our results suggest that tea plant responses to intense SAR stress incorporate three aspects: (1) stress resistance via altering metabolic pathways to enable survival; (2) stress avoidance via restraining uncontrolled non-stomatal gas exchange; and (3) stress escape via redistributing nitrogen from stress damaged leaves. These findings provide valuable insights into plant responses to acid rain stress. [ABSTRACT FROM AUTHOR]