The mesoporous yolk-shell nanoparticles (MYSNs), with a movable FeO core inside the hollow capsules, with two different morphologies (1) FeO@SiO@hollow@fibrous SiO (Yolk Shell-1) (2) FeO@SiO@hollow@mesoporousSiO (Yolk Shell-2) were fabricated as carriers for Candida rugosa lipase (CRL) immobilization, through a template-assistant selectively etching method. Firstly the hydrophilic FeO nanoparticles were synthesized according to the solvothermal method. Then, SiO shell was coated on the FeO nanoparticle surface by a sol-gel reaction. Subsequently, the resorcinol farmaldehyde (RF) shell was covered on the surface of as-prepared FeO@SiO composites and sandwiched FeO@SiO@RF composites were formed, which were finally provided with mesoporous fibrous (KCC) in the Yolk Shell-1 and mesoporous Silica in the Yolk Shell-2(Non fibrous). After selectively etching CTAB and the middle RF layer, the two kinds of yolk/shells composites were obtained. By utilization of their large and open mesopores (20-50nm) with good surface area (457.78-625.54m/g,) CRL was immobilized after amino functionalization using glutaraldehyde as a linker. The ICRL on Y.S-1, Y.S-2 showed good loading (797-501mg/g) and enzyme activity of (1503-837U/g) respectively. Thermal stability, resistance to pH, recycling and storage capacity were improved as compare to free lipase.