Assembling nanoparticles (NPs) into ordered architectures remains a challenge in the field of nanotechnology. Templated strategies have been widely utilized for NP assembly. As typical biological nanostructures, virus-based NPs (VNPs) have shown great promise in templating NP assembly. Here it is illustrated that the VNP of simian virus 40 (SV40) is a powerful scaffold in directing the assembly of 3D hybrid nanoarchitectures with one NP encapsulated inside as a core and a cluster of gold NPs (AuNPs) on the outer surface of the SV40 VNP as a shell, in which the core NPs can be CdSe/ZnS quantum dots (QDs), Ag2S QDs, or AuNPs. The assembling of AuNPs onto the SV40 VNP surface is determined by the interactions between the AuNPs and the amine groups on the outer surface of SV40 VNPs. It is expected that the VNP guided 3D hybrid nanoarchitectures provide ideal models for NP interaction studies and open new opportunities for integrating various functionalities in NP assemblies.