Lignocellulose-based hydrogels may have many potential applications in biomedical and biotechnological fields owing to their attractive properties including low cost, biodegradability, and biocompatibility. In this study, cellulose/lignin composite hydrogel beads were prepared by co-dissolution of cellulose and lignin in 1-ethyl-3-methylimidazolium acetate and then reconstitution with distilled water. Lipase from Candida rugosa was immobilized on various cellulose/lignin hydrogel beads. The results showed that lipase immobilized on cellulose/lignin beads showed higher activity and stability than those of lipase immobilized on pure cellulose beads. The activity and stability of immobilized lipase increased with the increase in the lignin content in the cellulose/lignin beads. The activity, protein loading, and specific activity of lipase immobilized on the optimal cellulose/lignin beads were 2.6, 2.2, and 1.2 times higher than those of lipase immobilized on cellulose beads, respectively. The effect of lignin on the activity of lipase immobilized on cellulose/lignin beads was statistically well predicted. The residual activity of lipase immobilized on the optimal cellulose/lignin beads after incubation for 12 h at 40 °C was 3.2 and 1.9 times higher than that of free lipase and lipase immobilized on cellulose beads, respectively. Interestingly, the half-life time of lipase immobilized on cellulose/lignin beads at pH 3.0 was 24 and 3 times higher than that of free lipase and that of lipase immobilized on cellulose beads, respectively. These results show that cellulose/lignin hydrogels may offer many potential applications in the biocatalytic, biomedical, and bioelectronic fields owing to their high biocompatibility, biodegradability, and controllable properties.