Greenhouse gas (GHG) emission from water surface nearby the small hydropower station is a rising problem of concern. This paper studied the daytime changes of GHG flux of Fujiang hydropower station (FJHPS) and Xiasi hydropower station (XSHPS) located on Qingshui river in Guizhou by the static float chamber sampling and the gas chromatography analysis method in Autumn. Data showed, the fluxes of CO2, CH4 and N2O ranged from −43 to 72, −23 to 15 and −0.016 to 0.13 mmol·(m2·d)−1, respectively. Overall, the GHG fluxes in the downstream of the station were slightly higher than the upstream, which manifested the downstream released more GHGs. The CO2 exchange fluxes in FJHPS were higher than XSHPS, while CH4 and N2O fluxes showed a reverse situation. The fluxes of GHG had a positive correlation with DO and pH. Compared with other lakes and reservoirs, smaller releasing rates of GHG were existed in the small hydropower station.