ABSTRACT Microcystis aeruginous were cultured to study on the algae organic matter (AOM) migration, transformation and potential to produce nitrogenous disinfection by-products (N-DBPs) during algae growth, dissolved organic nitrogen (DON) concentration shows an upward tendency. The migration of nitrogen in different inorganic ions were studied. Large molecular weight substances in EOM gradually transform into small molecules with the growth of algae, while the molecular weight distribution of IOM stay stable. EOM is mainly composed of humic acid-like materials and soluble microbial products, while IOM is mainly composed of aromatic proteins and soluble microbial products. The strongly hydrophobic organic matter (HPO) possesses the highest proportion. In IOM, but the hydrophilic fraction of IOM presents the highest N-DBPs formation potential. The hydrophilic organic matter (HPI) is the major content of EOM, but the HPO presents the highest N-DBPs formation potential.