In this review paper, the state-of-the-art knowledge of the core-shell multifunctional nanoparticles (MNPs), especially with unique physiochemical properties, is presented. The synthesis methods were summarized from the aspects of both the advantages and the demerits. The core includes the inexpensive and easily oxidized metals and the noble shells include the relatively noble metals, carbon, silica, other oxides, and polymers. The properties including magnetic, optical, anti-corrosion and the surface chemistry of the NPs are thoroughly reviewed. The current status of the applications is reviewed with the detailed examples including the catalysis, giant magnetoresistance (GMR) sensing, electromagnetic interface shielding or microwave absorption, biomedical drug delivery, and the environmental remediation.