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Wetlands are considered to be the important carbon sequestration functional units, and moisture is a critical environmental factor that affects the mineralization of soil organic carbon (SOC). However, little information is available on the effects of soil moisture on SOC mineralization in floodplain wetlands with different flooding frequencies. Soil samples to a depth of 20 cm were collected in five types of floodplain wetlands with different flooding frequencies (i.e., permanent floodplain F0, 1-year floodplain F1, 5-year floodplain F5, 10-year flood plain F10, and 100-year floodplain F100) in the downstream of the Huolin River basin of China. A 30-day incubation experiment with three moisture treatments (i.e., 30%, 60%, and 100% water holding capacity (WHC)) was used to identify SOC mineralization processes and key influencing factors in these five floodplain wetlands. Our results showed that the topsoils (0-10 cm) contained significantly higher SOC contents than the subsurface soils (10-20 cm). The SOC contents followed the order of F5 > F0 > F1 > F10 > F100 and the order FO > F5 > F100 > F1 > F10 in the topsoils and subsurface soils, respectively, of five floodplain wetlands. The optimum moisture for the SOC mineralization of the topsoils was 30% WHC in F100, and 60% WHC in the other four wetlands. In the case of all the subsurface soils, 30% WHC was the optimum moisture for the SOC mineralization. The mineralization processes of SOC (especially the active carbon pool) could be better fitted by first-order kinetic models (R-2 > 0.98). The topsoils basically showed a lower C-0/SOC ratio (C-0: the potentially mineralized carbon) than the subsurface soils, except in the case of 60% and 100% WHC in F0 and F5. Under higher soil moisture conditions, the mineralization parameter k was significantly correlated with soil conductivity (p < 0.05). Under low soil moisture condition, C-0/SOC showed significant correlations with soil pH (p < 0.01). Our findings indicate that the change in the soil moisture of floodplain wetlands with different flooding frequencies could greatly affect the carbon pool of inland wetlands.