【Objectives】The impact of greenhouse gas caused by the agricultural activities on global warming has been recognized broadly. The aim of this study was to evaluate the effects of different fertilizer treatment on greenhouse gas emissions,crop yield and soil fertility of paddy soil. 【Methods】The fertilization treatments were designed under the rice-wheat rotation system in Yangtze River as follows: no nitrogen fertilizer (CK),farmer's customary fertilization (FP),optimum N fertilization (OPT),OPT plus manure (OPT + M),and OPT plus wheat straw return (OPT + S). Static opaque chamber method was used to measure the CH_4,N_2O and CO_2 flux during the rice-growing season and the global warming potential (GWP). The crop yield,carbon emission intensity and soil chemical property of rice production (GHGI) were comprehensively evaluated and a fertilizer management system was proposed.【Results】1) The cumulative emission of CH_4 in different treatments was in order of OPT + S > OPT + M > FP > OPT > CK (99.02 -143.69 kg /hm~2),that of NO_2 was FP > OPT + M > OPT > OPT + S > CK (0.95 -3.57 kg /hm~2),and that of CO_2 showed the same trend as CH_4 's,ranging from 7231.64 to 13715.24 kg /hm~2. 2) Calculated as the CO_2-equivalents on the scale over 100 years,the GWP from the CH_4 and N_2O emissions in different treatments were in order of OPT + S > OPT + M > FP > OPT > CK. The contribution of N_2O to the total GWP were only 10.31%,26.39%,21.51%,22.91%,and 11.58%,and that of CH_4 were 89.69%, 73.61%,78.49%,77.09% and 88.42% in CK,FP,OPT,OPT + M and OPT + S respectively. The overall assessment of the GWP was dominated by CH_4 emissions and much lower by N_2O. The rice yield in treatment of OPT,OPT + M and OPT + S was 3.6%,14.3% and 8.5% more than in FP. The most significant yield increase was obtained in treatment of the combined application of organic manure with chemical fertilizer. 3) The GHGI was in order of FP(0.56) > OPT + S(0.52) > OPT(0.50) > OPT + M(0.49). The GHGI in treatment OPT and OPT + M were significantly lower than in FP,and the lowest value was in OPT + M. 4) The highest soil organic carbon, total nitrogen, available phosphorus and potassium content were all appeared in the OPT + S treatment. 【Conclusion】Fertilization influence the emissions of CH_4,N_2O and CO_2. The application of manure and chemical nitrogen fertilizer increase the emissions of all the three greenhouse gases,the straw return increases the emissions of CO_2 and CH_4,but reduces that of N_2O. Mitigation of CH_4 emissions should be considered in the paddy soil with priority. As the chemical fertilizer plus manure (OPT + M) produces the lowest GHGI,the pattern is recommended as relatively better fertilizer management in this region. Although the straw return will increase the emission of CO_2 from soil,it is still a prosperous management as it could reduce the total CO_2 emission from possible burning of straw. Further research on proper amount of straw return should be conducted.