Lignin heterogeneity, involving complex structure and high polydispersity, is a key challenge that restricts its value-added applications. Fractionation of heterogeneous lignin into several homogeneous subdivisions is an attractive and practical strategy to overcome this limitation. In this work, γ-valerolactone (GVL), a sugar-derived product, was used as a green solvent for lignin fractionation when mixed with water. The enzymatic hydrolysis lignin (EHL) was subdivided into three different fractions (F1, F2, and F3) by dissolving it completely in 60% aqueous GVL and then following gradient precipitation in 40%, 30%, and 5% aqueous GVL solutions, sequentially. Detailed characterization techniques were conducted to provide a comprehensive evaluation of the three obtained lignin fractions. Moreover, the proposed fractionation mechanism was further investigated on the basis of Kamlet–Taft parameters. The gel permeation chromatography (GPC) analyses showed that the three fractions presented lower polydispersity than the parent EHL and, furthermore, a gradual decreasing molecular weight due to the different solubility of various molecular weight lignins in aqueous GVL solvents. The structural analyses revealed that with the decrease of molecular weight, the guaiacyl unit content in lignin fractions decreased, with significant increases of functional groups (i.e., aromatic/aliphatic hydroxyl and carboxyl groups). The solvent recycling study showed that the aqueous GVL had a high recovery, and the recycled GVL had the same lignin fractionation performance as fresh GVL. Overall, compared with traditional fractionation using multiple organic solvents, the present work provides a green and efficient route to fractionate lignin and, therefore, significantly decreases its molecular weight polydispersity and structural heterogeneity.