The precise control of the size, morphology, surface chemistry, and assembly process of each component is important to construction of integrated functional nanocomposites. We report here the fabrication of multifunctional microspheres which possess a core of nonporous silica-protected magnetite particles, transition layer of active gold nanoparticles, and an outer shell of ordered mesoporous silica with perpendicularly aligned pore channels. The well-designed microspheres have high magnetization (18.6 emu/g), large surface area (236 m(2)/g), highly open mesopores (approximately 2.2 nm), and stably confined but accessible Au nanoparticles and, as a result, show high performance in catalytic reduction of 4-nitrophenol (with conversion of 95% in 12 min), styrene epoxidation with high conversion (72%) and selectivity (80%), especially convenient magnetic separability, long life and good reusability. The unique nanostructure makes the microsphere to be a novel stable and approachable catalyst system for various catalytic industry processes.