A field experiment was conducted to study the dynamics of dissolved organic carbon (DOC), readily oxidizable organic carbon (ROC), and microbial biomass carbon (MBC) in a paddy soil under integrated rice-duck farming (RD), intermittent irrigation (RW), and conventional flooded irrigation (CK), the three rice farming modes typical in southern China. Under these three farming modes, the soil DOC and MBC contents reached the highest during the period from rice booting to heading, while the soil ROC content had less change during the whole rice growth period. Two-factor variance analysis showed that soil MBC was greatly affected by rice growth stage, soil DOC was greatly affected by rice growth stage and farming mode, and soil ROC was mainly affected by farming mode. Comparing with CK, RD significantly increased the soil DOC and ROC contents and their availability, while RW significantly decreased the soil DOC content and its availability but increased the soil ROC content and its availability. No significant differences were observed in the soil MBC and microbial quotient among RD, RW, and CK.