Lignin, a by-product of pulping and biorefinery, has great potential to replace petrochemical resources for wastewater purification. However, the defects of lignin, such as severe heterogeneity, inferior reactivity and poor solubility, characterize the production process of lignin-based products by high energy consumption and serious pollution. In this study, several lignin fractions with relatively homogeneous structure were first obtained by organic solvent fractionation, and their structures were fully deciphered by various characterization techniques. Subsequently, each lignin component was custom-valued for wastewater purification based on their structural characteristics. Benefiting from the high reactivity and reaction accessibility, the lignin fraction (lignin-1) refined by dissolving in ethanol and n-butanol could been used as a raw material to produce cationic lignin-based flocculant (LBF) in a copolymerization system using green, cheap and recyclable ethanol as solvent. The lignin fraction (lignin-2) extracted by methanol and dioxane showed low reactivity and high carbon content, which was used to produce lignin-based activated carbon (LAC) with phosphoric acid as activator. Moreover, the influences of synthetic factors on the purification capacity were discussed, and the LBF and LAC produced under the optimal conditions showed distinguished purification effect on kaolin suspension and heavy metal wastewater, respectively. Furthermore, the corresponding purification mechanism and external factors were also elaborated. It is believed that this cleaner production strategy is helpful for the valorization of lignin in wastewater resources.