This study investigated five persistent organic pollutants (polychlorinated and polybrominated dibenzo-p-dioxins (PCDDs/PBDDs), dibenzofurans (PCDFs/PBDFs), biphenyls (PCBs/PBBs), and diphenyl ethers (PBDEs)) in ash collected from several units (super heater (SH), heat economizer (HE), semi-dryer absorber (SDA), bag-house filter (BF), and fly ash pit (FAP), and bottom ash (BA) discharger) of a large-scale municipal solid waste incinerator (MSWI). Data on levels and emission factors of the five target compounds in the different units of the MSWI were first reported. The PCDD/Fs were found in high content in the HE, mainly because of the operating temperature range (250–400°C) which is favorable for PCDD/F formation through de novo synthesis. High concentrations PCBs and PBBs were detected in the BF. The highest concentrations of PBDD/Fs and PBDEs were observed in the BA. A significant correlation existed between content of PCDD/F and PCB in individual ash and corresponding operating temperature, while the content of ash-bound PBDD/Fs and PBDEs chiefly related to feeding wastes that contained brominated flame retardants. The emission of the five pollutants in the MSWI was primarily from fly ash. Further treatment is necessary for ash collected from the HE and BF because the ash had total-PCDD/F content exceeding the regulation limit (1 ng I-TEQ/g) in Taiwan.