Total concentrations (11.8–29.3 ng I-TEQ/g approximately) of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in the fly ash discharged from a laboratory waste incineration process (375 kg/h) have frequently been found to exceed the limit set by Taiwan’s EPA (1.0 ng I-TEQ/g).PCDD/Fs can generally be decomposed in incineration chambers at the temperature range of 1173–1273 K. The main objective of this work was thus to determine how the PCDD/Fs in fly ash are formed when the incineration flue gas is cooling down. The results show that concentrations of total (290 mg/kg) and leachable (9.4 mg/L) copper in the deposited ashes on the internal walls of the cooling towers are greater than those of other toxic elements. To better understand how the relatively high PCDD/Fs concentrations in the cooling towers and bag filter ashes are associated with copper species during the cooling process of the flue gas, the chemical structure of these were studied by synchrotron X-ray absorption near edge structure (XANES) spectroscopy. Notably, it seems that a high fraction of CuO in the cooling tower ashes may lead to relatively high PCDD/F concentrations in the fly ashes. In contrast, copper in the form of CuSO4 may depress the formation of PCDD/Fs. The correlation of molecule-scale data for copper species with the PCDD/F concentrations of ashes in the commercial-scale waste incineration process can provide useful information for the reduction of PCDD/F.