Feeding rate is an important factor influencing the carbon and nitrogen input and greenhouse gas emission from aquaculture systems. However, the quantitative relationship between feeding rates and GHG emissions is still poorly understood. In this study, we conducted a laboratory-scale experiment to examine the impact of feeding rate (0%, 2%, 4%, 6%, and 8%) on the CH4 and N2O emissions from a pond rice-fish co-culture system. The results showed that the total amount of CH4 emission did not significantly differ when the feeding rate was no more than 6%, but increased more than four times when the feeding rate reach to 8%. The amount of N2O emission showed a linearly increasing trend with the feeding rate. The emission factors of CH4 and N2O was significantly higher for 8% feeding rate than other feeding rates. The variation of CH4 emission was primarily attributed to the ratio of mcrA/pmoA in the sediment and the contents of biological oxygen demand (COD) and dissolved oxygen (DO) in the water; and the variation of N2O was primarily affected by the available nitrogen in the water and sediment and the content of DO in the water. The overall emission of CH4 and N2O showed an exponential relationship with feeding rate. The total yields of fish and rice did not continuously increase when the feeding rate exceeded 4%. The lowest emission intensity per unit yield was reached at the feeding rate of 2.99%. These results can provide a reference for the determination of low-carbon feeding strategy for pond rice-fish co-culture system.