The emissions of pollutants by waste-to-energy power plants, which contain more toxic substances owing to the complicated composition of municipal solid waste (MSW), such as NOx, SO2, HCl, HF, particulate matter, and heavy metals, has attracted increasing attention worldwide. To effectively control the pollutants, a flue gas cleaning system is indispensable in the operation of MSW incineration power plants. In this study, the flue gas cleaning system in a waste-to-energy power plant with flue gas recirculation (FGR) was evaluated. The concentrations of various pollutants were measured and compared with the standards at home and abroad. The results indicated that NOx emission can be effectively reduced by FGR, and that the emission concentration of NOx may meet the national emission standards only by adopting FGR. However, the emission levels of HCl and PM exceeded the limits in legislative standards; therefore, operation optimization or retrofit of a deacidification system and bag filter were proposed to comply with the international standards and near-zero-emissions goal.