Yolk-shell structure with magnetic core, interior void and mesoporous polymer/carbon shell demonstrate potential applications in biocatalysis, magnetic biological separation, biomedicine, and magnetic resonance imaging due to their comprehensive benefits of magnetic and mesoporous shells. Herein, yolk-shell structured magnetic mesoporous polydopamine microspheres (Fe 3 O 4 @Void@mPDA) and the corresponding derivatives of carbon-based microspheres (Fe 3 O 4 @Void@mCN) are successfully fabricated through an interface assembly and selective etching approach. The obtained monodisperse Fe 3 O 4 @Void@mPDA microspheres consist of a magnetic core, a mesoporous polydopamine shell, and the large void formed between them, with perpendicular mesopores (5.2 nm), high surface area (303.3 m 2 g -1 ), and richness of functional groups. The Fe 3 O 4 @Void@mPDA microspheres show a remarkable inhibitory effect on tumor cells. Moreover, the Fe 3 O 4 @Void@mCN microspheres can immobilize ultrafine Au nanoparticles for hydrogenation of 4-nitrophenol with superb catalytic activity and excellent magnetic reusability.