Virus-based nanoparticles (VNPs) can serve as containers for inorganic nanomaterials with excellent physical and chemical properties. Incorporation of nanomaterials inside the inner cavity of VNPs has opened up lots of possibilities for imaging applications in the field of biology and medicine. Encapsulation of inorganic nanoparticles (NPs) in VNPs can achieve the labeling of VNPs with nanoprobes and maintain the original outer surface features of VNPs at the same time. In return, VNPs enhance the stability and biocompatibility of the inorganic cargoes. This review briefly summarizes the current typical strategies to encapsulate inorganic nanomaterials in VNPs, i.e. mineralization and self-assembly, as well as the applications of these hybrid nanostructures in the field of bioimaging, including and fluorescence imaging, magnetic resonance imaging, and theranostics. Nanophotonic studies based on the VNP platform are also discussed. We anticipate that this field will continue to flourish, with new exciting opportunities stemming from advancements in the rational design of VNPs, the development of excellent inorganic nanomaterials, the integration of multiple functionalities, and the regulation of nano-bio interfacial interactions.