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The effects of simulated acid rain (SAR) on the photosynthetic performance of subtropical coniferous species have not been thoroughly investigated. In this study, we treated two coniferous species, <i>Pinus massoniana</i> (PM) and <i>Cunninghamia lanceolata</i> (CL), with four gradients of SAR and then analyzed their photosynthetic activities through measurements of gas exchange, prompt fluorescence (PF), delayed fluorescence (DF), and modulated reflection at 820 nm (MR₈₂₀). Gas exchange analysis indicated that the decrease in the net photosynthetic rate (Pn) in PM and CL was unrelated to stomatal factors. For the PF transients, SAR induced positive K-band and L-band, a significant reduction in photosynthetic performance index (PI_ABS), the quantum yield of electron transfer per unit cross-section (ET_O/CS_m), and maximal photochemical efficiency of photosystem II (F_v/F_m). Analysis of the MR₈₂₀ kinetics showed that the re-reduction kinetics of PSI reaction center (P700⁺) and plastocyanin (PC⁺) became slower and occurred at later times under SAR treatment. For the DF signals, a decrease in the amplitude of the DF induction curve reduced the maximum value of DF (I₁). These results suggested that SAR obstructed photosystem II (PSII) donor-side and acceptor-side electron transfer capacity, impaired the connectivity between PSII and PSI, and destroyed the oxygen-evolving complex (OEC). However, PM was better able to withstand SAR stress than CL, likely because of the activation of a protective mechanism.