Anthropogenic NOx, SO2 and CO2 emission from the fossil-fuel-fired power plants has aroused growing attention. This study investigated the removal performance of CO2, SO2 and NOx in flue gas as well as conversion efficiency of nitric- and sulfur-compounds in liquid phase in a biofilter. In order to develop the potential of the biofilter, simulative industry wastewater was employed as the spray solution. The satisfactory flue gas removal performance (75.23% CO2, 100% SO2 and 82.81% NO) were achieved under the optimal operating conditions of biofilter: initial solution pH of 9 and liquid-gas ratio (L/G) of 3. The gas film mass transfer coefficients (kGa) results showed that the resistance of gas mass transfer was decreased with increasing the pH value and L/G ratio, respectively. The final transformation product of NO was mostly N2 while about 78% SO2 was converted to elemental sulfur. The microbial community analysis results showed that the relative abundance of bacteria with denitrification capacity was increased by 3.05% which might have contributed to the conversion of NO intermediates products in present study. Collectively, this biofilter system achieve a better flue gas removal performance via the proper operation system, which provides an economic feasible strategy of flue gas purification and increases potential for industrial application.