To provide scientific basis for rational fertilization in double rice, effects of organic–inorganic fertilizer application on soil enzyme activities, microorganism activities, microbial biomass carbon (SMBC) content, microbial biomass nitrogen (SMBN) content, organic matters content and carbon pool management index were studied in double rice paddy field for four–year experiments. Six kinds of fertilizers were applied in this study, 1) without fertilizer(WF), 2) without N (WN), 3) chemical fertilizer only (CF), 4) pig manure alternative 20% N fertilizer (ZF), 5) pig manure compost alternative 20% N fertilizer (DF), 6) biogas slurry and biogas residue alternative 20% N fertilizer (ZYF). The results showed that soil quality were differences among different organic–inorganic applications with the best performance from DF treatment. Compared with CF treatment after 4 years, soil culturable amount of bacterial, fungi, actinomyces, the contents of the SMBC and SMBN in DF treatment were increased by 67.94%, 50.30%, 55.51%, 17.96% and 50.17% respectively, and the activities of soil phosphatase, urease, invertase and cellulase were increased by 18.19%, 7.85%, 73.47% and 105.00%. In addition, the contents of soil total organic and activity organic and carbon pool management index were increased by 15.17%, 58.40% and 71.98%. In conclusion, with pig manure compost–inorganic fertilizer application, soil enzyme activities were significantly improved, and the amount of culturable bacterial, fungi and actinomyces were increased significantly and also the contents of the SMBC, SMBN and carbon pool management index were highly promoted. Thus, organic manure and chemical fertilizers combined application, especially DF treatment, is helpful to enlarge soil carbon pool and improve soil quality.