NAD+-dependent Cα-dehydrogenase LigD and glutathione-dependent β-etherase LigF which selectively cleave the β-O-4 aryl ether linkage present in lignin, are key-enzymes for the biocatalytic depolymerization of lignin. However, the catalytic efficiency of the two enzymes is low when they are used to break down the β-aryl ether linkage in natural lignin. When sulfonated lignin was added to LigF hydrolysis reactions, the conversion rate of MPHPV decreased significantly from 99.5% to 32.6%. On the contrary, sulfonated lignin has little affection on LigD, which the conversion rate of GGE only decreased from 41.7% to 41%. The strong nonspecific interactions of enzymes onto sulfonated lignin detected by surface plasmon resonance (SPR) and isothermal titration calorimetric (ITC) was obvious and universal, which can reduce enzyme activity of many enzymes, including ligninolytic enzyme β-etherase LigF. To elucidate the exact mechanisms by which β-etherase LigF interact with lignin, molecular modeling was applied. Finally, analysis on catalytic efficiency of LigD and LigF in different concentrations and molecular weights of sulfonated lignin, solution ionic strength, pH, temperature and concentration of Tween 80 revealed that electrostatic interactions and hydrophobic interactions play important roles in absorption between LigF and sulfonated lignin.