Proteins were the main category of the dissolved organic nitrogen (DON) in eutrophicate water sources and posed a threat to the water quality safety and common operation of water plants, while the KMnO4 pre-oxidation and coagulation were the two important ways to control the organics. Intracellular organic matter (IOM) and phycocyanin were chosen as the target DON to study the performance of KMnO4 pre-oxidation to the enhanced removal effects for coagulation process, and molecular weight distribution, hydrophobicity, two-dimensional electrophoresis and MnO2 adsorption experiment were used to study the mechanism. The results showed that KMnO4 pre-oxidation enhanced the IOM and phycocyanin removal performance of coagulation significantly, although poor removal was found for KMnO4 oxidation alone. KMnO4 pre-oxidation altered the molecular weight, hydrophobicity and proteins' categories insignificantly. However, the in-situ formed MnO2 showed better adsorption ability for the IOM and phycocyanin. The main enhanced removal mechanism was the adsorption of MnO2 formed from the reduction of KMnO4 and little difference existed between the IOM and phycocyanin. In addition, the KMnO4 pre-oxidation could enhance the turbidity removal of the coagulation due to a similar mechanism.