Rivers connect continent and ocean, the two major carbon pools, which play an important role in global carbon cycling. Jinsha River is the upstream of Yangtze River and significantly influences carbon cycle and chemical weathering in the watershed. Water-air CO₂ and CH₄ fluxes were measured from August 8 to 18, 2015 in the downstream of Jinsha River. The study used the headspace equilibrium method and thin boundary layer method to estimate p(CO₂) and p(CH₄) in surface water and exchange fluxes between water and air. Results showed that in summer p(CO₂) and CO₂ fluxes were 2724.84±477.18 μatm and 2.24±0.50 mmol/(m²·h), respectively, the p(CH₄) and CH₄ fluxes were 59.96±6.74 μatm and 0.000163±0.00009 mmol/(m²·h), and the trend of differential pressure was consistent with flux. p(CO₂) has significant positive correlation with dissolved inorganic carbon and total alkalinity. p(CH₄) has significant positive correlation with water temperature and chlorophyll-a. Air-water CO₂ fluxes was mainly impacted by p(CO₂), dissolved inorganic carbon and total alkalinity. CH₄ fluxes was significantly impacted by p(CH₄) and wind speed. Impacts from other environmental factors such as nutrients were not obvious, and more studies shall be conducted to elucidate the variance of flux and its controlling factors. The air-water CH₄ fluxes of Jinsha River was low, and the air-water CO₂ fluxes was in medium level, comparing to other major rivers in the world.