In this paper, we investigated the functional imaging and targeted therapeutic properties of core@multi-shell nanoparticles composed of a superparamagnetic iron oxide (SPIO) core and gold nanorods (GNRs) in the mesoporous silica shells functionalized with folic acid (FeO@SiO@GNRs@mSiO-FA). The as-synthesized five-component hybrid nanocomposite was revealed to have insignificant cytotoxicity. Intracellular uptake of the nanoparticles was studied in the folate receptor over-expressing human epidermoid carcinoma of the nasopharynx (KB) cells. Due to their magnetic/optical properties as well as the folate targeting potential, compared with FeO@SiO@GNRs@mSiO nanoparticles, higher cellular uptake efficiency was observed for FeO@SiO@GNRs@mSiO-FA nanoparticles in KB cells. Characterizations were achieved using both dark field and magnetic resonance (MR) imaging techniques. The hyperthermia induced by FeO@SiO@GNRs@mSiO-FA nanoparticles resulted in a higher cytotoxicity in KB cells. Thus, the FeO@SiO@GNRs@mSiO-FA hybrid nanomaterial is an effective and promising MR imaging and photothermal therapy agent for folate-receptor over-expressing cancer cells.