Chlorine dioxide is widely used for pulp bleaching because of its high delignification selectivity. However, efficient and clean chlorine dioxide bleaching is limited by the complexity of the lignin structure. Herein, the oxidation reactions of phenolic (vanillyl alcohol) and non-phenolic (veratryl alcohol) lignin model species were modulated using chlorine dioxide. The effects of chlorine dioxide concentration, reaction temperature, and reaction time on the consumption rate of the model species were also investigated. The optimal consumption rate for the phenolic species was obtained at a chlorine dioxide concentration of 30 mmol·L−1, a reaction temperature of 40 °C, and a reaction time of 10 min, resulting in the consumption of 96.3% of vanillyl alcohol. Its consumption remained essentially unchanged compared with that of traditional chlorine dioxide oxidation. However, the consumption rate of veratryl alcohol was significantly reduced from 78.0% to 17.3%. Additionally, the production of chlorobenzene via the chlorine dioxide oxidation of veratryl alcohol was inhibited. The structural changes in lignin before and after different treatments were analyzed. The overall structure of lignin remained stable during the optimization of the chlorine dioxide oxidation treatment. The signal intensities of several phenolic units were reduced. The effects of the selective oxidation of lignin by chlorine dioxide on the pulp properties were analyzed. Pulp viscosity significantly increased owing to the preferential oxidation of phenolic lignin by chlorine dioxide. The pollution load of bleached effluent was considerably reduced at similar pulp brightness levels. This study provides a new approach to chlorine dioxide bleaching. An efficient and clean bleaching process of the pulp was developed.