Rivers serve as a crucial link between the ocean and terrestrial ecosystems. Research on greenhouse gas emissions from reservoirs has predominantly focused on tropical and cold-temperate regions, while few on carbon emissions in subtropical regions. This study investigates the carbon flux (CO2 and CH4) at the water–air interface in the Lancang River Basin, a representative subtropical mountainous area, by analyzing gas samples collected using the floating static chamber method at 26 sites along the main and tributary streams during the dry season (April) and the rainy season (August). The aim is to reveal the temporal and spatial variations of carbon emissions at the water–air interface in the Lancang River Basin. The results indicate that: (1) emission fluxes of CO2 and CH4 are higher in the dry season than those in the rainy season. (2) The carbon fluxes at the water–air interface are higher in the middle and lower reaches of the main stem than those in the upper reaches. Additionally, carbon fluxes downstream of hydropower stations are higher than those upstream. (3) Mean values of carbon fluxes in tributaries are generally higher than those in main stream spatially, associated with higher CO2 fluxes during the rainy season and higher CH4 fluxes within dry season temporally in tributaries.