Enzymatic hydrolysis of lignocellulose for bioethanol production shows a great potential to remit the rapid consumption of fossil fuels, given the fact that lignocellulose feedstocks are abundant, cost-efficient, and renewable. Lignin results in low enzymatic saccharification by forming the steric hindrance, non-productive adsorption of cellulase onto lignin, and deactivating the cellulase. In general, the non-productive binding of cellulase on lignin is widely known as the major cause for inhibiting the enzymatic hydrolysis. Pretreatment is an effective way to remove lignin and improve the enzymatic digestibility of lignocellulose. Along with removing lignin, the pretreatment can modify the lignin structure, which significantly affects the non-productive adsorption of cellulase onto lignin. To relieve the inhibitory effect of lignin on enzymatic hydrolysis, enormous efforts have been made to elucidate the correlation of lignin structure with lignin–enzyme interactions but with different views. In addition, contrary to the traditional belief that lignin inhibits enzymatic hydrolysis, in recent years, the addition of water-soluble lignin such as lignosulfonate or low molecular-weight lignin exerts a positive effect on enzymatic hydrolysis, which gives a new insight into the lignin–enzyme interactions. For throwing light on their structure–interaction relationship during enzymatic hydrolysis, the effect of residual lignin in substrate and introduced lignin in hydrolysate on enzymatic hydrolysis are critically reviewed, aiming at realizing the targeted regulation of lignin structure for improving the saccharification of lignocellulose. The review is also focused on exploring the lignin–enzyme interactions to mitigate the negative impact of lignin and reducing the cost of enzymatic hydrolysis of lignocellulose.