The effects of Mn(II) on Fenton system to treat papermaking wastewater and the mechanism of Mn(II) enhanced Fenton reaction were investigated in this study. The chemical oxygen demand (COD) removal efficiency was enhanced in the presence of Mn(II), which increased by 19% compared with that of the Fenton system alone. The pseudo-first order reaction kinetic rate constant of Mn(II)/Fenton system was 2.11 times higher than that of Fenton system. 67%–81% COD were removed with the increasing Mn(II) concentration from 0 to 0.8 g/L. COD removal efficiency was also enhanced in a wider pH range (3–7), which indicated the operation parameters of Fenton technology could be broadened to a milder condition. The study of the mechanism showed that Mn(II) participated in the oxidation and coagulation stages in Fenton system. In the oxidation stage, Mn(II) promotes the production of HO2•/ O2•−, then HO2•/ O2•− reacts with Fe(III) to accelerate the formation of Fe(II), and finally accelerates the production of HO•. Meantime MnMnO3 and Fe(OH)3 forms in the coagulation stage, facilitating the removal of suspended substances and a large amount of COD, which enhances the overall COD removal of papermaking wastewater. This study provided a detailed mechanism to improve practical applications of Fenton technology.