Understanding the dynamics of soil organic carbon (SOC) in response to changing environment and management practices is crucial for minimizing the climatic impacts of rice agriculture. This study examined the effects of rice straw incorporation on total SOC, active SOC fractions, and carbon pool management index (CPMI) in a subtropical paddy field in China. The straw collected after harvesting the early and late paddy was incorporated immediately into the top 10 cm soil at a rate of 3.3 Mg ha−1 and the top 40 cm soil samples in the triplicate treatment, control and reference plots were analyzed for the concentrations of total SOC and four other active SOC fractions at the end of the early and late seasons. The concentrations of total soil organic carbon (SOC), light fraction organic carbon (LFOC), dissolved organic carbon (DOC), and microbial biomass carbon (MBC) were significantly (P < 0.05) higher in the straw application plots than in the controls by 7.1–128.6% for both the early and late paddy season. In general, significant and positive correlations were observed between SOC, DOC, LFOC, MBC and labile organic carbon (LOC) in the treatment and control plots for both early and late paddy (r = 0.60–0.96, P < 0.05). Moreover, there were significant and positive correlations of total SOC and active SOC fractions with both soil water content (r = 0.69–0.94, P < 0.01) as well as total soil nitrogen content (r = 0.69–0.99, P < 0.05). Straw incorporation significantly increased CPMI and other active soil organic carbon pools in the early paddy field (P < 0.05), but had no significant effects on CPMI in the late paddy field. It is therefore better to incorporate straw residues in the aerobic condition during the early paddy season in order for rice to benefit from an increased CPMI.