In this paper, the antimicrobial effect of inert flue gas on indicator microorganisms in ballast water was investigated based on a 265h test. The inert flue gas consists of nitrogen (N_2) and carbon dioxide (CO_2) the microorganisms include Chlorella and Escherichia coli. Within the scope of the test, the killing effect of the microbes treated by combining N_2 and CO_2 was higher than that of using only either N_2 or CO_2. When the dissolved oxygen concentration in the ballast water was 0.5 mg/L and the pH value was 6, the killing effect was the highest. At this time, the mortality rate of Chlorella sp. and E. coli reached 99.99%, and 99.98%, respectively. After the experiment, property of the ballast water treated by N_2 and CO_2 were analyzed. The dissolved organic carbon concentration was lower than the recommended minimum concentration of 5 mg/L. The concentration of particulate organic carbon was higher than the standard value of 0.3%.The experiment proposes a new method for ballast water treatment of large ocean-going vessels in the future.