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Atmospheric deposition of nitrogen (N) and phosphorus (P) far exceeding the pre-industrial levels have the potential to change carbon (C) dynamics in northern peatlands. However, the responses of soil C concentration and organo-chemical composition to different rates and durations of nutrient enrichment are still unclear. Here, we compared the short- (3 years) and long-term (10 years) effects of N and P fertilizations on the physicochemical properties of peat and porewater in a bog-fen complex in northern China. Our results showed that the short-term fertilization increased Sphagnum moss cover, while the expansion of vascular plants was observed owing to the long-term fertilization. The preserved soil C did not vary considerably after the short- and long-term fertilizations. The harsh soil conditions may impede the decomposition of organic matters by soil microorganisms during the short-term fertilization. For the long-term fertilization, the input of high-phenolic litters owing to vascular plant expansion likely exerted an important control on soil C dynamics. These processes constrained the variation in soil C concentrations when the addition rate and cumulative amount of external N and P increased, which will advance our understanding and prediction of the resilience of soil C storage to imbalanced nutrient enrichment of N and P in northern peatlands.