Abstract: Inland rivers are hotpots for the exchange of greenhouse gases(GHGs) with the atmosphere and have a significant influence on global carbon cycle. GHGs(CH4 and CO2) emission from waters of the riparian zone of middle and lower reaches of Yangtze River was measured during the normal season of 2017 and flood season of 2018. Results showed that the fluxes of CH4 and CO2 across the water-air interface ranged from 0.39 to 9668.83 nmol·m-2·h-1 and 0.25 to 3 229.41 μmol·m-2·h-1 in normal season, respectively, while -22.80 to 329.76 nmol·m-2·h-1 and -110.21 to 16.39 μmol·m-2·h-1 in wet season, respectively, for CH4 and CO2. Water temperature, pH, total dissolved phosphorus, and C/N ratio were important influencing factors on CH4 and CO2 fluxes. In addition, the fluxes of CH4 and CO2 at river-connected areas were significantly higher than at lake-connected areas. Due to differences in the external pollutions and land use characteristics, urban zones showed the highest CH4 and CO2 fluxes, followed by natural, wetland and estuarine zones. Industrial areas showed the lowest CH4 and CO2 fluxes. An annual carbon emission of middle and low reaches of Yangtze River was dominated by CO2, with an estimation of 1.93×107 t(C)/a, while only 2.28×104 t(C)/a for CH4. Compared to other large rivers, the estimation value of annual carbon emission of Yangtze River was relatively lower.