Co-incineration of medical waste (MW) in municipal solid waste incinerators (MSWIs) is a crucial disposal method for emergency disposal of MW and the management of MW in small and medium-sized towns. This study aims to analyze and compare the levels and distribution patterns of chlorine/brominated dioxins and their precursors in fly ash from MSWIs and medical waste incinerators (MWIs) while also focusing on identifying the new pollution concerns that may arise from the co-incineration of municipal solid waste (MSW) mixed with MW (MSW/MW). The concentration of chlorobenzene (CBzs), polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) in fly ash from co-incineration of MSW/MW are 887.4, 134.4 and 27.6 μg/kg, respectively, which are 5.1, 2.0 and 2.9 times higher than that from MSWIs. The levels of polybrominated dibenzo-p-dioxins/dibenzofurans (PBDD/Fs) are about three orders of magnitude lower than that of PCDD/Fs. For the fly ash from MSWIs, the predominant PCDD/Fs congener is OCDD, which prefers synthesis and adsorption on fine-grained fly ash. For fly ash from MWIs, the major PCDD/Fs congeners are 1, 2, 3, 4, 6,7, 8-HpCDF, and OCDF, which prefer synthesis and adsorption on coarse-grained fly ash. Correlation analysis exhibited that both 1,2,3-TriCBz and 1,2,4-TriCBz in fly ash have a markedly linear correlation with PCDD/Fs and PCBs, but PBDD/Fs shows a poor negative correlation with PCDD/Fs. Display omitted •Co-incineration can significantly increase CBzs, PCBs, and PCDD/Fs levels.•The levels of PBDD/Fs are around 1/1000 of PCDD/Fs.•Distributions of Cl/Br-substituted dioxins in size-classified fly ash were studied.•PBDD/Fs shows a poor negative correlation with PCDD/Fs.