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Due to the emissions of air pollutants, acid rain in southern China poses a great threat to terrestrial ecosystems. However, its influences on ecological processes such as litter decomposition and soil organic carbon (SOC) accumulation are still not clear. The aim of this study was to understand the potential mechanisms of carbon sequestration change in response to long-term acid rain in a subtropical forest. A field experiment with simulated acid rain (SAR) treatment was conducted in a monsoon evergreen broadleaf forest in southern China. Four levels of SAR treatment were implemented by irrigating the plots with water of different pH values (4.5 as a control, 4.0, 3.5, and 3.0). The results showed that the concentration of SOC and recalcitrant index for the SAR pH = 3.0 treatment were significantly higher compared to the control. Lignin fractions in litter residue layers were significantly increased, while soil microbial biomass carbon and soil ligninolytic enzyme activities were reduced under the SAR treatment. The concentration of SOC and recalcitrant index had positive relationships with the litter residue lignin fraction, but negative relationships with soil ligninolytic enzyme activity. These findings indicate that soil carbon accumulation could be enhanced with more stable lignin input under prolonged acid rain in forest ecosystems in southern China.