Agricultural ecosystems are globally important sinks of carbon and other nutrient elements. In China, acid rain events affect about 0.62 million km², representing about 6.4% of total land area; however, the impacts of acid rain mediated nitrogen (N) and sulfur (S) depositions on soil organic carbon (SOC) fractions and nutrient stocks in paddy soils and implications for yield production under climate change are unclear. We conducted a field experiment during two annual crop seasons to determine the effects of simulated acid rain on SOC fractions and nutrients in a subtropical paddy in China. Acid rain treatments comprised solutions of HNO₃ + H₂SO₄ to simulate N and S deposition at pH levels of 4.5, 3.5, and 2.5. The results showed that content of soil C fractions varied with acid rain pH. Acid rain led to increased SOC concentrations and decreased the ratios of soil labile organic carbon (LOC): SOC and dissolved organic carbon (DOC): SOC concentrations, independently of crop season and growth stage. Soil salinity was positively associated with SOC suggesting that higher levels of salinity inhibit C decomposition favoring SOC accumulation. Treatment effects of acid rain on soil microbial C and N depended on crop growth stage. Concentration of Fe²+ was positively correlated with DOC in early and late paddy soils under acid rain, possibly as a result of Fe²+ retention by DOC, when Feᶟ+ is reduced to Fe²+. Acid rain led to increases in soil TN, TP, available N, NH4+ concentration, and SOC, and decreases in ratios of DOC: SOC, indicating decreases in soil biological activity and mineralization processes. Increases in dead rice plant biomass under acid rain were consistent with the increase in soil N and P concentrations, due to reduced nutrient uptake, and higher levels of total SOC.