Jerusalem artichoke (Helianthus tuberosus L.) is emerging as one of the energy plants considered for biofuel production. Alkali and alkali-involved pretreatment methods have been widely used for the bioconversion of cellulosic materials due to their high sugar yield and low inhibitor release. However, the recovery and treatment of wastewater (black liquor) have been poorly studied. Here, we present a novel two-stage pretreatment process design for recycling black liquor. Jerusalem artichoke stalk (JAS) was first treated with 2% (w/v) NaOH, after which lignin was recovered by H2SO4 at pH 2.0 from the black liquor. The recycled solutions were subsequently used to treat the NaOH-pretreated JAS for the second time to dissolve hemicellulose. CO-pretreated JAS, hydrolysates, and acid-insoluble lignin were obtained after the above-mentioned two-stage pretreatment. A reducing sugar yield of 809.98 mg/g Co-pretreated JAS was achieved after 48 h at 5% substrate concentration using a cellulase dosage of 25 FPU/g substrate. In addition, hydrolysates containing xylose and acid-insoluble lignin were obtained as byproducts. The pretreatment strategy described here using alkali and acid combined with wastewater recycling provides an alternative approach for cellulosic biorefinery.