Model estimation is one of the main method in greenhouse gas flux monitoring of water-air interface, which has made many achievements. However, many environmental factors will be uncertain influence on the final result in the process of monitoring. In Pengxi River of Three Gorges Reservoir, the water-gas interface greenhouse gas flux (CO₂, for example) was estimated with the model estimation, and the local sensitivity analysis fixed Morris screening method was carried out for all the parameters in model estimation on greenhouse gas diffusion flux. The research shows that the model estimation is used to calculate greenhouse gas flux on water-air interface in Pengxi River, Three Gorges Reservoir has high feasibility and reliability; wind velocity, water temperature and pH value will affect the monitoring results. And the stronger the wind speed, the higher the water temperature, the smaller the pH value, the greater the CO₂ diffusion flux; The pH value is a highly sensitive parameter, while wind speed and water temperature are sensitive parameters. In the monitoring process in Pengxi River of Three Gorges Reservoir, the instrument should be corrected in order to ensure the accuracy of pH value before sampling.