Co-immobilize enzyme by cross-linking and embedding, optimize conditions for immobilizing, determinate the enzymatic properties of co-immobilized enzyme and study the methods for preparation of genipin using co-immobilized enzyme to hydrolyze geniposide. Optimized immobilizing conditions include glutaraldehyde concentration being 0.15%, cross-linking temperature being 20°C, cross-linking time being 2 hours, the activity of co-immobilized β-glucosidase and cell reaches to 65.33U/mg and the enzyme activity recovery being 52.63%. Enzymatic properties of co-immobilized enzyme are following: optimum temperature is 55°C and optimum pH is 5.0. The transformation experiments are carried out with co-immobilized enzyme. The results show that half-life of co-immobilized enzyme reaches around 40 days, higher than the normal immobilized enzyme. The conversion rate of geniposide is above 95% after 8 hours. The genipin is isolated, purified and recrystallized to reach more than 98% of purity by High Performance Liquid Chromatography. Advantages to prepare genipin using co-immobilized enzyme include low cost, high yield, environmental friendly and easy to manufacturing.