Concentrations and distributions of PAHs and chlorinated aromatic compounds including PCDD/Fs, dl-PCBs, chlorophenols (CPs), and chlorobenzenes (CBz) in the municipal waste incinerator are investigated to characterize their formation and emission via intensive stack sampling. In addition, the toxicity of fly ash contribution by PCDD/Fs and dl-PCBs is evaluated in this study. The results reveal that concentrations of PCDD/Fs and dl-PCBs in flue gas are significantly lower than those of CPs, CBz, and PAHs. Additionally, the removal efficiencies of PAHs and chlorinated aromatic compounds achieved with existing air pollution control devices are evaluated, indicating that the removal efficiencies achieved with activated carbon injection + baghouse (95–99%) are higher than those with semi-dry scrubber (SDS). Besides, PCDD/Fs and PCBs TEQ concentrations in SDS and BH ashes are within 1.61–2.66 WHO-TEQ/g and 0.09–0.19 WHO-TEQ/g, respectively. Furthermore, the calculated mass flow rates suggest that the input rate of PCDD/Fs and dl-PCBs of SDS are 60.24 mg/h and 59.74 mg/h, respectively. The mass flow rates of PCDD/Fs and dl-PCBs after SDS in flue gas are 32.47 mg/h and 49.73 mg/h, respectively. However, the discharge rates of PCDD/Fs and dl-PCBs from SDS are 120.60 mg/h and 27.05 mg/h, respectively, indicating that PCDD/Fs are significantly formed within the SDS. PCDD/Fs formation is attributed to the operating temperature of SDS (240 ± 11.5 °C), which is within the temperature window for de novo synthesis. Thus, operating parameters of the APCDs should be optimized to reduce the formation of PAHs and chlorinated aromatic pollutants from MWI.