The controllable self-assembly of inorganic nanoparticles (NPs) into larger specific structures provides an effective route for the fabrication of new materials with unique optical, electronic, and magnetic properties. In particular, the incorporation of inorganic NPs into polymeric assemblies can endow them with new advanced functionalities (e.g. plasmonic and magnetic properties), while preserving the well-established properties of the organic components. Inspired by self-assembly in nature, we have been devoted to design synthetic polymer-inorganic hybrid nanocompartments that mimic viral capsids from the aspects of such as surface, topology, and mechanical properties. These nanostructures may find applications in biological imaging, controlled drug/gene release, biosensors, and catalysis. This talk will present a new paradigm to the organization of nanoparticles into a diverse range of complex hierarchical nanostructures by controlling the thermodynamic or kinetic pathways of assembly, and some preliminary experimental results demonstrating their biomedical applications including remote-controlled release, photo-thermal therapy, and two-photon luminescence imaging.