Pre-oxidation has been reported to be an effective way to remove algal cells in water, but the released algal organic matter (AOM) could be oxidized and lead to the increment in disinfection by-product (DBP) formation. The relationship between pre-oxidation and AOM-derived DBP formation needs to be approached more precisely. This study compared the impact of four pre-oxidants, ozone (O3), chlorine dioxide (ClO2), potassium permanganate (KMnO4) and sodium hypochlorite (NaClO), on the formation of nitrogenous (N-) and carbonaceous (C-) DBPs in AOM chlorination. The characterization (fluorescent properties, molecular weight distribution and amino acids concentration) on AOM samples showed that the characterization properties variations after pre-oxidation were highly dependent on the oxidizing ability of oxidants. The disinfection experiments showed that O3 increased DBP formation most significantly, which was consistent with the result of characterization properties variations. Then canonical correspondent analysis (CCA) and Pearson's correlation analysis were conducted based on the characterization data and DBP formation. CCA indicated that C-DBPs formation was highly dependent on fluorescent data. The formation of haloacetic acids (HAAs) had a positive correlation with aromatic protein-like component while trichloromethane (TCM) had a positive correlation with fulvic acid-like component. Pearson's correlation analysis showed that low molecular weight fractions were favorable to form N-DBPs. Therefore, characterization data could provide the advantages in the control of DBP formation, which further revealed that KMnO4 and ClO2 were better options for removing algal cells as well as limiting DBP formation.