The invention discloses a system and a method for measuring carbon dioxide emission factors of a power station boiler. The system comprises an automatic flue gas tester and other power station boiler devices, wherein the automatic flue gas tester is accessed to be arranged on three cross sections (9, 10 and 11). The method comprises measuring carbon dioxide emissions of the three cross sections and obtaining the carbon dioxide emission factors of the power station boiler through calculation by a weighing algorithm. According to the system and the method for measuring the carbon dioxide emission factors of the power station boiler, the system structure is simple, the method facilitates operation and calculation, measured data are representative, and the measured carbon dioxide emission factor data are accurate.