With the rapid development of industry and transportation, air pollution is worsening, therefore, monitoring of air pollution components is more and more heeded. In this study, based on the measurement model and the composition of the air quality monitoring system on line, the mathematical model of the measurement system value transmission was analyzed, and the uncertainty components were calculated respectively, a conclusion that the main factor of the overall system uncertainty is the uncertainty of system itself in the existing air quality monitoring system was drawn, so measurement uncertainty of the calibration system was focused on the research. The effects of the Zero-gas, calibration gases and gas mass flow controller on the uncertainty of the calibration system was experimented and analyzed, and measurement uncertainty of the dynamic calibration system was evaluated.