To improve the performance of lipase in biosynthesis of benzyl cinnamate, a new immobilized lipase by entrapping enzyme into nano-molecular cages was designed. Consequently, the entrapped lipase showed a robust immobilization, which diminished the leakage of lipase notably in use. Moreover, the entrapped lipase exhibited higher activity (57.1 U/mg) than free lipase (50.0 U/mg), demonstrating that the native conformation of lipase was not destroyed during immobilization. Compared with the adsorbed lipase (half-life 40.7 min) and free lipase (half-life 29.8 min), the entrapped lipase (half-life 85.3 min) increased the stability by about 2-3 times. Furthermore, the entrapped lipase was applied in biosynthesis of benzyl cinnamate, where it showed excellent activity and re-usability. After 7 cycles, the yield of benzyl cinnamate catalyzed by the entrapped lipase remained 70.2%, while the yield catalyzed by the adsorbed lipase was only about 10%. These results indicated that the nano-molecular cages could inhibit denaturation of lipase and maintain its activity well.