Copper [Cu(II)] can dominate the disinfection byproduct (DBP) formation derived from algal organic matter (AOM). However, the influential mechanism of Cu(II) in the formation of DBP at the molecular level remains largely unknown. In this study, we investigated the reaction between AOM and chlorine as well as the effect of Cu(II) on the reaction characteristics between AOM and chlorine by two-dimensional correlation spectroscopy (2DCOS) analysis. Extracellular and intracellular organic matter (EOM and IOM) showed significant differences in DBP formation. This result could be explained by the fact that fulvic-like and aliphatic compounds in EOM preferentially reacted with chlorine to form TCM; on the contrary, tryptophan-like and aromatic compounds in IOM showed the highest chlorine activity, thus generating a large amount of DCAN. Cu(II) increased the formation of TCM in EOM, whereas it repressed TCM formation during IOM chlorination. The binding of Cu(II) to fluorophores and functional groups altered the reactivity of AOM with chlorine, thus affecting DBP formation. Furthermore, the high concentration of Cu(II) showed a significant effect on the reaction between various chemical structures of AOM and chlorine. This study presents new insight into the role and behavior of Cu(II) in DBP formation.