An extensive evaluation on a modern full-scale municipal solid waste incineration system was conducted for characterizing the distribution of highly toxic chlorinated aromatics, polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs) and polychlorinated naphthalenes (PCNs), and their corresponding mass fluxes in post combustion zone. It was found that the flue gas/fly ash partitioning behaviors of chlorinated aromatics could be essentially described by their octanol-air partition coefficients (KOA) and strongly affected by the flue gas temperature. Above 93% of chlorinated aromatics formed in boiler section was partitioned into the flue gas and transported into the subsequent flue gas cleaning system, in which above 92% of Cl3–8DDs, Cl3–7DFs, Cl5–10Bs and Cl4–8Ns in flue gas was removed by the discharge of fly ash. The results of mass flux calculation indicated that the memory effect in flue gas cleaning system remarkably elevated the emission levels of chlorinated aromatics, especially the less chlorinated ones. The memory effect should mainly result from the direct chlorination mechanism mediated by the deposited particles. In addition, activated carbon injection could cause an obvious increase in PCBs emission. The obtained results provided some important implications for further reducing the emission of highly toxic chlorinated aromatics.