Recycling agricultural residues is a promising strategy to enhance soil organic carbon (SOC) and improve soil quality. This study investigated the effects of exogenous organic carbon (EOC) amendments—straw and hydrochar—on SOC, its labile fractions, and the carbon pool management index (CPMI, an indicator of soil carbon quality and management efficiency) under flooding (FI) and controlled irrigation (CI) in a two-year pot experiment using paddy soil under field conditions. CI improved the soil average readily oxidizable organic carbon (ROC), dissolved organic carbon (DOC), and microbial biomass carbon (MBC) by 6.37–12.19%, 18.70–26.00% (p < 0.05), and 11.95–17.97% (p < 0.05), compared to FI. Similarly, EOC addition increased average ROC, DOC, and MBC during the entire rice growth period by 12.33–22.95%, 4.50–24.35%, and 6.24–21.51%, respectively, compared to the unamended controls. Additionally, CI increased soil carbon lability (L), carbon pool activity index (LI), carbon pool index (CPI), and CPMI by 3.39–14.01%, 3.65–8.84%, 1.75–2.58%, and 6.19–16.01%, respectively, although some of these increases were not statistically significant. Notably, the combination of CI and EOC application significantly increased CPMI by 19.45–20.29% (p < 0.05), with the highest values observed in CI treatments amended with either straw or hydrochar. Hydrochar application had a smaller effect on increasing soil active OC fractions compared to straw incorporation, but demonstrated a greater potential for long-term SOC sequestration. These findings demonstrate the potential of hydrochar as a waste-derived amendment for long-term carbon sequestration and provide insights for optimizing water–carbon management strategies in sustainable rice cultivation.