Using fermentable sugars from lignocelluloses to produce chemicals and fuels is a way to resolve the energy crisis and environmental problems, but nonproductive adsorption of cellulase onto lignin is big challenge for bioconversion of cellulose to fermentable sugars. As cellobiohydrolase (CBH) is the main enzyme in cellulase mixture, understanding the adsorption mechanism of CBH onto lignin is important to enhance CBH catalytic efficiency by avoiding the nonproductive adsorption. This study suggested that CBH displayed high adsorption affinity to lignin, especially for the lignin isolated from liquid-hot-water pretreated substrate, and a stable combination of lignin-CBH was formed. The CBH adsorbed to lignin still had the catalytic ability on Avicel, although the ability was decreased. The possible reason, by molecular docking, was that the catalytic domain of CBH was irreversibly adsorbed onto lignin mainly through a hydrophobic cleft located oppositely to catalytic tunnel, not influencing the catalytic process of the enzyme except for the protein movement. Electrostatic interaction played a significant role in the adsorption of carbohydrate binding domain (CBM) of CBH to lignin. Altering the charges from positive to negative of amino acid on the CBM of CBH by engineering enzyme may be a feasible way to reduce the adsorption affinity of CBH onto lignin.