A preliminary study shows that lysine production from lignocellulose feedstock is feasible, but the conversion of xylose in lignocellulose to lysine remains unsolved. Two technical barriers are responsible for the remaining xylose conversion: one is the xylose loss into the wastewater stream of the biorefinery processing chain, and the other is the lack of efficient lysine-producing strain with xylose utilization. Here, we conducted a new biorefinery approach of consequent dry acid pretreatment and biodetoxification, resulting in zero wastewater generation and then well-preserved xylose. To provide the lysine-producing strain with xylose utilization, we modified the Corynebacterium glutamicum by establishing the xylose assimilation pathway and improving the NADPH cofactor regeneration. The combinational modification of biorefinery processing and strain development led to 31.3 g/L of lysine production with a yield of 0.23 g lysine per gram of wheat straw derived sugars. This study provides a practical method for upgraded lysine production from lignocellulose for future industrial applications.