Biomolecular nanostructures in nature are drawing increasing interests in the field of materials sciences. As a typical group of them, virus-based nanoparticles (VNPs), which are nanocages or nanorods assembled from capsid proteins of viruses, have been widely exploited as templates to guide the fabrication of complex nanoarchitectures (NAs), because of their appropriate sizes (ca. 20–200 nm), homogeneity, addressable functionalization, facile modification via chemical and genetic routes, and convenient preparation. Foreign materials can be positioned in the inner cavity or on the outer surface of VNPs, through either direct synthesis or assembling preformed nanomaterials. Simultaneous use of the inner and outer space of VNPs facilitates integration of multiple functionalities in a single NA. This review briefly summarizes the strategies for fabrication of NAs templated by VNPs and wide applications of these NAs in fields of catalysis, energy, biomedicine, and nanophotonics, etc.