Mineralization of soil organic carbon (SOC) and nitrogen (N) plays an important role in maintaining soil quality and providing nutrients for crop growth. However, the response of carbon (C) and N mineralization to fertilization strategies and their relationship with soil structure are not clear. In this study, the effects of different fertilization strategies on the mineralization of SOC and N of a paddy soil were analyzed based on a long-term field experiment. The relationship between carbon (C) and N mineralization and the water stability of soil aggregates was also studied. The field experiment had 4 fertilization treatments: no fertilizer (CK), chemical fertilizer (NPK), double chemical fertilizer (NPK2) and chemical fertilizer plus organic manure (NPKOM). Results showed that NPKOM treatment significantly increased SOC and total nitrogen (TN) contents compared to CK; however, no significant difference was found between the treatments of chemical fertilizers (NPK2 and NPK) and CK treatments. The mineralization rates, cumulative mineralization and mineralization ratio of SOC all showed the same trend as NPKOM>NPK2>NPK>CK, where NPKOM treatment was significantly higher than other treatments while there was no significant difference among NPK2, NPK and CK treatments. The mineralization rates, cumulative mineralization, and N mineralization ratio showed the same trends as SOC. Compared with CK treatment, NPKOM, NPK2 and NPK treatments increased N cumulative mineralization by 110.0%, 29.4% and 8.8% respectively, and increased N mineralization rate by 110.8%, 25.6% and 13% respectively. Compared to CK treatment, the mean weight diameter (MWD) of water-stable aggregates of NPK2 and NPK treatments decreased by 17.1% and 15.5%, respectively, while NPKOM treatment increased MWD by 19.4%. Correlation analysis shows that the mineralization of SOC and N mainly depended on SOC and N content, and was not correlated with the water stability of soil aggregates. Future research should focus on the effect of soil pore structure on the turnover of SOC and N.