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Understanding the interactions between lignin and cellulase enzymes will help better design biomass pretreatment and enzymatic hydrolysis processes. Ethanol organosolv lignins (EOLs) were isolated from organosolv pretreatment of sweetgum (SG) and loblolly pine (LP) under different temperature. The structural changes of EOLs were determined by 13C NMR and HMBC NMR to elucidate their positive and/or negative effects on enzymatic hydrolysis. Alkylation of lignin with ethanol in organosolv pretreatment resulting in the etherification of Cα was observed in both EOL-SG and EOL-LP. The effect of EOL-SG on enzymatic hydrolysis was correlated with the content of ethoxyl group. The lignin alkylation in EOLs appeared to be reversible at high temperature, resulting in the inverse change of their effects on enzymatic hydrolysis. A strong correlation was observed between the binding affinity of cellulases onto EOLs and their corresponding hydrolysis yields. Lignin alkylation likely reduce the affinity of enzyme onto lignin, which can enhance the enzymatic hydrolysis.