A 1000 Nm3/h capacity pilot scale dual baghouse filter system was tested on flue gas and fly ash from a municipal solid waste incinerator, and the removal efficiency of dioxins, heavy metals and HCl was studied. Activated carbon was injected at the inlet of the first baghouse filter to remove the gas phase dioxins and heavy metals, and baking soda was injected at the inlet of the second baghouse filter to remove HCl. Concentrations of dioxins at the outlet of the first and second baghouse were 0.034 and 0.011 ng TEQ/Nm3, respectively, which were both far below the national emission standard. The particulate matter concentration was 0.85 mg/m3, and the heavy metals leaching concentration of the fly ash from the second baghouse filter was lower than the hazardous waste identification standard. HCl concentration was almost zero at the outlet of the second baghouse filter when the optimal equivalence ratio of baking soda to HCl was 1.6. In addition, the estimated fly ash yield was 2.35% of the incinerated solid waste for the dual baghouse filter system, which was significantly lower than 3.5% as the traditional semidry scrubber + single baghouse filter.