Methane (CH_4) and nitrous oxide (N_2O) are two of the most important greenhouse gases. The concentrations of CH_4 and N_2O in the atmosphere have been increasing since the industrial revolution. The paddy field N_2O emissions account for 7%-11% of the farmland N_2O emissions. Therefore, it is important to research the origin and dynamic of CH_4 and N_2O emissions under which different fertilization conditions are applied. To investigate the effects of the same carbon level of organic fertilizer applications on methane and nitrous oxide emissions in paddy soils, various organic manures were used in a three-year (2010-2012) study. They were: chemicals fertilizer (CF), pig manure +chemicals fertilizer (PM), chicken manure + chemicals fertilizer (CM), and rice straw + chemicals fertilizer (RS). Control was paddy field without fertilizer (NF). The greenhouse gas emission was measured by using the static chamber-gas chromatography method. The results showed that the CH_4 seasonal emission of CF treatment was 202.1, 279.9 and 332.5 kg/hm~2. There was no significant difference (P>0.05) between CF and NF in CH_4 seasonal emission, and significant difference (P<0.05) between CF and CM, RS. N_2O emission from CF treatment was 1.12, 1.26 and 1.29 kg/hm~2. There were no significant differences (P>0.05) among CF and the other three organic manures in N_2O seasonal emission. Furthermore, the CH_4 emission was effected by paddy soil Eh value, temperature, and organic carbon contents, such as the readily oxidizable organic carbon. The CH_4 emissions had a negative correlation with soil Eh value, but a positive correlation with soil temperature at 5 cm soil depth. The liable carbon contents in the organic manures ranged from 18.4 to 114.5 g/kg. ROC_(167) (ROC_(167) is defined as carbon that can be readily oxidized by 167 mmol/L of potassium permanganate in manures) had a significant impact on CH_4 emission and showed a positive correlations between CH_4 emission and ROC_(167) content with a correlation coefficient of 0.872 (P<0.05). The average yields of rice production were increased by 14.3% (P<0.05) in fields applied with organic fertilizers for the third years than those applied with CF only. Among the three different organic manure treatments, global warming potential (GWP) and greenhouse gas intensity (GHGI) are the lowest in the PM treatment, which may be due to low content of ROC_(167) in the PM. There were no significant differences among PM, CF and NF in GWP and GHGI. In summary, PM could balance the relationship between environmental concerns of CH_4 and N_2O emissions and rice production concern of increasing yield. Treatment of PM could be recommended as a valuable CH_4-limiting organic fertilizer for future use in rice paddy fields.