Noble metal Au nanoparticles have attracted extensive interests in the past decades, due to their size and morphology dependent localized surface plasmon resonances. Their unique optical property, high chemical stability, good biocompatibility, and easy functionalization make them promising candidates for a variety of biomedical applications, including bioimaging, biosensing, and cancer therapy. With the intention of enhancing their optical response in the near infrared window and endowing them with additional magnetic properties, Au nanoparticles have been integrated with other functional nanomaterials that possess complementary attributes, such as copper chalcogenides and magnetic metal oxides. The as constructed hybrid nanostructures are expected to exhibit unconventional properties compared to their separate building units, due to nanoscale interactions between materials with different physicochemical properties, thus broadening the application scope and enhancing the overall performance of the hybrid nanostructures. In this review, we summarize some recent progresses in the design and synthesis of noble metal Au-based hybrid inorganic nanostructures for nanomedicine applications, and the potential and challenges for their clinical translations.