The positive linear relationship between qCO2 and cumulative CO2 confirmed that the positive PE is mainly driven by decreasing CUE owing to low nutrient inputs. Similarly, negative PE after high nutrient input was mainly driven by the increased CUE. The effect of nutrient availability on SOM decomposition was also supported by the increased net C:N ratio of mineralized SOM pools under low nutrient addition and decreased net C:N ratio under high nutrient addition treatments. We conclude that low nutrient (N, P, K, Ca, and S) addition stimulate C losses, whereas high nutrient addition facilitates C sequestration in paddy soils.