The lignin can compete for binding cellulase enzymes with cellulose fibers and decrease the accessibility of enzymes to carbohydrates. The competitive adsorption of cellulase to lignin mainly depended on the chemical structure of lignin. The post-pretreatment can decrease the lignin content and modify the lignin structure of pretreated substrates, which reduced the lignin inhibition on enzymatic saccharification. Therefore, the post-treatment by modifying the lignin structure would attract considerable attention for weakening the cellulase–lignin interactions. Three modified lignins, including sulfonated lignin (SL), oxidized lignin (OL), and carboxylated lignin (CL), were prepared from alkali lignin (AL) and their structures and physicochemical properties were characterized using FTIR, NMR, XPS analysis, zeta potential, and contact angle, respectively. Compared to AL, three modified lignin preparations exhibited the decrease in contact angle by 61–70% and phenolic hydroxyls content by 17–80%, and an obvious increase of negative charges by about 21–45%. This was mainly due to the drop of condensation degree and the incorporation of carboxylic and sulfonic acid groups into modified lignins. Langmuir adsorption isotherms showed that the affinity strength between cellulase and modified lignins significantly reduced by 54–80%. Therefore, the 72 h hydrolysis yield of Avicel with SL, OL, and CL was 48.5, 51.3, and 49.4%, respectively, which was increased 8–15.3% than that of Avicel with AL, 44.5%. In the enzymatic hydrolysis of bamboo biomass, the glucose yield at 5 d was 38.5% for AS-P. amarus, 15.4% for AO-P. amarus and 21.4% for AC-P. amarus, respectively, which were 1.4–3.5 times of alkali pretreated P. amarus. The post-treatment can weaken the nonproductive adsorption between lignin and cellulase proteins and improve the enzymatic saccharification efficiency. This study will provide a conceptual combination of pretreatment technologies and post-pretreatment by modifying lignin structure for reducing the cellulase–lignin interaction.