Display omitted •IOM chemical structure was rich in aromatic and aliphatic protein-like materials.•EOM contained humic and fulvic-like substances with high carboxylic content.•Chemical structure of IOM had high reactivity to substitute with chlorine.•IOM was a higher-yielding precursor of THMs and HAAs than EOM. Algal eutrophication in reservoirs is frequently accompanied by a remarkable increase in the concentration of algogenic organic matter (AOM). Because AOM is well-known as an important precursor to disinfection byproducts (DBPs) in drinking water, algal eutrophication poses severe concerns for public health. This study aimed to characterize the chemical properties of AOM from two major origins, i.e. extra- (EOM) and intra-cellular organic matter (IOM), of a commonly found green alga Chlorella sp. as precursors to trihalomethanes (THMs) and haloacetic acids (HAAs). Particularly, the corresponding relation between the chemical functional structure of EOM and IOM and their THM and HAA formation potential (THMFP and HAAFP) was comprehensively investigated. Results show that IOM chiefly comprised of aromatic and other aliphatic protein-like materials (high organic nitrogen content) those have high activity for chlorine substitution (high UV253/UV203 value) due to the high hydroxyl and amide contents in its chemical structures. EOM alternatively exhibited the characteristics of humic- and fulvic-like materials accompanying with high DOC/DON ratio and aromaticity. However, the chemical structure of EOM had a low tendency for chlorine substitution (low UV253/UV203 value); it was also accompanied by a considerable content of carboxylic moisture, which likely resulted in an unfavorable substitution reaction of EOM with chlorine. As a result, the carbonaceous DBP formation potential (C-DBPFP) showed that IOM yielded higher levels of both THMFP and HAAFP than that yielded by EOM.