Converting lignin into value-added products in current lignocellulosic biorefineries has been challenging, which in turn restricts the commercialization of many lignocellulosic biorefineries. In this work, a two-stage alkalioxygen assisted liquid hot water pretreatment (AlkOx) was proposed as the first step of biorefinery. This alkalioxygen pretreatment facilitated biomass fractionation by solubilizing majority of lignin in water-soluble fraction, while remaining most of cellulose and hemicellulose in water-insoluble fraction. As a result, biomass saccharification was significantly improved by selective removal and oxidative modification of lignin through alkalioxygen pretreatment. Moreover, lignin residues from both pretreatment hydrolysate and enzymatic hydrolysate were shown to be favorable adsorbents for Pb(II) ions, with adsorption capacity of 263.16 and 90.91 mg/g, respectively. Results demonstrated that this integrated process could not only improve biomass saccharification but also enable lignin valorization, which encouraged the holistic utilization of lignin residues as part of an integrated biorefinery.