Wet desulfurization is dominant in China’s coal power industry as flue gas discharged from wet desulfurization is over-saturated, includes lots of moisture, and can bring huge interference to the measurement of SO2. When using existing SO2 measuring methods, especially wet desulfurization technology aiming at ultra-low emissions, it is necessary to take into account the impact of water in flue gas. The pH value of condensate water of flue gas after desulfurization with limestone gypsum wet desulfurization is 2, lower than that of desulfurizing slurry, indicating that some SO2 has been dissolved in the water carried by flue gas after desulfurization. In order to avoid the interference of water, infrared online continuous emission monitoring system (CEMS) is equipped with a water removal device. When a conventional condensate water removal method is applied, condensate water will dissolve SO2 and then lead to the relatively low concentration of SO2 in the flue gas measured. When a proper water removal method is adopted, it can effectively avoid the measuring error as a result of SO2 dissolved in condensate water.