Magnetic nanocubes, with a controlled precursor molar concentration of ferric nitrate fixed at 0.004 M to ferrous chloride ranging from 0.002 to 0.01 M, were synthesized by a new simple colloidal method at 60 °C under 1 M alkaline condition. The metallic Au-ultrathin layer was successfully functionalized on the magnetic nanocubes surface for the fabrication of the core–shell structure (Fe3O4@Au) by the borohydrate reduction of HAuCl4 in water/poly-L-histidine solution. The functionalized core–shell structure with varying molar-ratios of Fe3+/Fe2+ in aqueous media, core–shell structural characteristics (for example, size, morphology, and shell thickness), and physical properties (for example, crystalline, electronic, optical, and magnetic ones) of the resultant functional nanocubes were systematically investigated using UV-visible spectroscopy, SEM, TEM, XRD, XPS, EDX, and superconducting quantum interface device (SQUID) magnetometer analysis. The core–shell structure of Fe3O4@Au exhibits plasmonic properties with high magnetization and showed excellent hyperthermia-photothemal activity towards the cancer cell (HeLa) killing. For the hyperthermia killing of cancer cells under the alternating current magnetic field (AMF), the as-prepared Fe3O4 exhibited higher activity than the Fe3O4@Au nanoparticles. Interestingly, under the simultaneously combined AMF and photoirradiation with Fe3O4@Au, much higher cancer cell killing was found than with only AMF induced hyperthermia killing. The promoting effect of an Au-ultrathin shell supported on Fe3O4 showed strong absorption in the visible region due to localized surface plasmon resonance and increased the hyperthermia-photothermal temperature with the photothermal stability of the Fe3O4@Au nanoparticles, rather than only Fe3O4. It was found that the cell killing activity depends on the optical and magnetic properties of the Fe3O4@Au nanocubes. The optical and magnetic properties depended on the molar-concentration ratios of precursors of Fe(NO3)3·9H2O and FeCl2·4H2O. The synthesized Fe3O4@Au nanocubes have great potential for a combination of cancer imaging and local treatment as a cancer cell killing paradigm of “see and treat” applications.