Dilute lignin solution was successfully digested into colorless and clarified liquor under microwave-assisted oxidative digestion with hydrogen peroxide. High dosage of hydrogen peroxide is needed to effectively digest lignin, but excessive hydrogen peroxide may lead to recondensation of formed fragments in digested lignin. Microwave irradiation greatly facilitates the oxidative digestion of lignin. Compared with conventional heating technique, microwave-assisted digestion achieves the same or higher digestion rate within a shorter time and/or at lower temperature. After digestion, total organic carbon content of lignin solution decreases by 93.9%, and a small amount of aliphatic alkane, alcohol, acid and ester are formed via the cleavage of aromatic rings as well as the deprivation of side chains in original lignin. This work provides an alternative way to efficiently treat spent pulping liquor.