Algae organic matters (AOM), including intracellular organic matters (IOM) and extracellular organic matters (EOM), are causing numerous water quality issues, among which formation of disinfection byproducts (DBPs) and odor & taste (O&T) compounds are of particular concern. In this study, physiochemical properties of IOM and EOM of Microcystic aeruginosa under an exponential growth phase (2.01 × 1011/L) were comprehensively characterized. Moreover, the yields of DBPs during AOM disinfection and O&T-causing compounds were quantified. Hydrophilic organic matters accounted for 86% and 63% of DOC in IOM and EOM, respectively. Molecular weight (MW) fractions of IOM in <1 kDa, 40–800 kDa, and >800 kDa were 27%, 42%, and 31% of DOC, respectively, while EOM primarily contained 1–100 kDa molecules. Besides, a low SUVA (0.84 L/mg m) and the specific fluorescence spectra suggested that AOM (especially IOM) was principally comprised of protein-like substances, instead of humic-like matters. The formation potentials of chloroform, chloroacetic acid, and nitrosodimethylamine were 21.46, 68.29 and 0.0096 μg/mg C for IOM, and 32.44, 54.58 and 0.0189 μg/mg C for EOM, respectively. Furthermore, the dominant O&T compound produced from EOM and IOM were 2-MIB (68.75 ng/mg C) and β-cyclocitral (367.59 ng/mg C), respectively. Of note, dimethyltrisulfide became the prevailing O & T compound following anaerobic cultivation.