The demands of energy sustainability drive efforts to bio-chemical conversion of biomass into biofuels through pretreatment, enzymatic hydrolysis, and microbial fermentation. Pretreatment leads to significant structural changes of the complex lignin polymer that affect yield and productivity of the enzymatic conversion of lignocellulosic biomass. Structural changes of lignin after pretreatment include functional groups, inter unit linkages and compositions. These changes influence non-productive adsorption of enzyme on lignin through hydrophobic interaction and electrostatic interaction as well as hydrogen bonding. This paper reviews the relationships between structural changes of lignin and enzymatic hydrolysis of pretreated lignocellulosic biomass. The formation of pseudo-lignin during dilute acid pretreatment is revealed, and their negative effect on enzymatic hydrolysis is discussed.