The emissions factors of PCDD/Fs from the stack flue gas, bottom ash and fly ash of a municipal solid waste incinerator (MSWI) were analyzed in this study. The congner profiles of PCDD/F mass were dominant in OCDD and OCDF; however, those of PCDD/Fs-TEQ were mainly 2,3,4,7,8-PeCDF and 1,2,3,7,8-PeCDD in all samples. The PCDD/F emission factors of MSWI per metric ton of waste incinerated from the stack flue gas, bottom ash and fly ash were at an averaged of 0.0919, 7.20 and 12.8 μg PCDD/Fs-WHO2005-TEQ ton–1, respectively. Futhermore, the emission factor of MSWI in the unit of electricity produced averaged 0.185, 14.5 and 26.3 μg PCDD/Fs-WHO2005-TEQ (MWh)–1, respectively. As the results shown in this study, the majority of total PCDD/Fs-WHO2005-TEQ were mainly in both bottom ash and fly ashes. From long-term perspective, the disposal of both bottom and fly ashes should pay more attention to this issue. The results of this study provide useful information for both further studies and environmental control strategies aimed at persistent organic compounds (POPs).