Lignin, which is considered one of the most recalcitrant components, limits the enzymatic hydrolysis of cellulose. When ball-milled lignin from switchgrass ranging from 21.4 to 64.3 mg/mL was added to a cellulose substrate (Avicel), the glucose release decreased from 17.4 to 22.4% compared to the hydrolysis rate of zero lignin addition. However, the cellulose decreasing conversion was reduced to 8.5% with 21.4 mg/mL ammonia fiber expansion (APEX)-treated lignin addition, as a result of the structural modification by AFEX pretreatment. The inhibitory effect of lignin was stronger on cellulose hydrolysis than on hemicellulose hydrolysis. The results showed that the free lignin released from biomass reduced the impact of the added lignin and that the AFEX pretreatment intensity was the key factor in increasing the enzymatic efficiency. The lignin structural modifications by AFEX pretreatment, such as slight increases in the molecular weight, degree of polymerization, and syringyl/guaiacyl ratio, reduced the lignin inhibition with a concomitant increase in the hydrolysis of cellulose.