Chlorinated halobenzoquinones (HBQs) widely exist in drinking water as emerging disinfection byproducts (DBPs), which have attracted significant attention due to their wide occurrence and high toxicity. In this study, the formation of chlorinated HBQs from the three free aromatic amino acids, tryptophan (Trp), tyrosine (Tyr) and phenylalanine (Phe), during chlorination was investigated, the formation pathways of chlorinated HBQs were explained based on the detected intermediates and influence factors. The results revealed that four chlorinated HBQs, including 2,6-dichloro-1,4-benzoquinone (2,6-DCBQ), 2,3,5-trichloro-1,4-benzoquinone, 2,3,5,6-tetrachloro-1,4-benzoquinone and 2,6-dichloro-3-methyl-1,4-benzonquinone, were formed in chlorination of the three free aromatic amino acids, and 2,6-DCBQ was the dominant species among the formed chlorinated HBQs. Of the three free aromatic amino acids, Trp and Tyr presented relatively high yields of chlorinated HBQs than Phe. Moreover, ten intermediates were successfully detected (e.g., N,2-dichloroaniline from Trp, 2,4,6-trichlorophenol from Tyr) according to the isotope and fragment information obtained using high resolution mass spectrometry. The formation pathways of chlorinated HBQs from Trp and Tyr were proposed to include electrophilic addition, electrophilic substitution, oxidation, deacidification and dehydration reaction, and further validated using theoretical calculation. The yields of chlorinated HBQs during chlorination of the free aromatic amino acids were significantly affected by free chlorine dosage, pH and temperature.