Agricultural soil carbon storage and carbon sequestration are the important issue of global change and carbon cycle. Paddy soil is major using types of agricultural soil in China. Soil labile organic carbon and carbon management index (CMI) are a good indicator to describe soil quality and evaluate soil management level. So study of the effects of the long-term fertilization on soil labile organic carbon, soil carbon management index in red paddy soil and rice yield has important practical significance. Based on the 33-year field experiment, research was conducted on effects of different fertilization on carbon management index and double rice yield in red paddy soil. Five treatments were set in the experiment, which included control (CK), N fertilizer (N), combined application of N and P fertilizer (NP), combined application of N, P and K fertilizer (NPK), combined application of inorganic and organic fertilizer (NPKM). The results indicated that the order of soil organic carbon, the labile organic carbon and carbon management index in different fertilizations was NPKM>NPK>NP>N>CK in red paddy soil. The content of soil organic carbon increased by 42.05%~60.23% in application of chemical fertilizer treatments, and which increased by 70.35% in NPKM treatment. The application of chemical fertilizer had no significant effect on content of soil labile organic carbon, but NPKM treatment had significant effect on them. Compared with CK, the content of soil microbial biomass carbon, dissolved organic carbon, labile organic carbon and particulate organic carbon in different treatments increased by 13.19%~67.70%、2.11%~23.41%、2.42%~99.37%、 8.18%~31.27% respectively, and the effect of combined application of organic and inorganic fertilizers is better than that of single fertilizer application. Soil carbon management index had increased in different degrees in long-term fertilization treatments, the application of chemical fertilizer had no significant effect on carbon management index, but NPKM treatment had significant effect on them. The order of annual production of double rice in different fertilization treatments was NPKM>NPK>NP>N>CK, the maximum annual yield of double rice increased by 109.87%~118.8% in NPKM treatment, and the rice yield of late rice was higher early rice. Therefore, the combined application of organic and inorganic fertilizers played an important role in the high and stable yield of rice and the improvement of carbon pool management index.