Molybdenum disulfide (MoS2), due to high surface area, excellent photothermal heat, and strong absorbance in near-infrared (NIR) region, is used extensively as a photothermal agent for biomedical applications. In this paper, we reported a nanoplatform based on MoS2 nanoflakes decorated with super-paramagnetic iron oxide magnetic nanoparticle (Fe3O4) (MoS2–Fe3O4 nanocomposite) to increase emission photothermal heat of MoS2 nanoflakes and it is used as a target moiety directed by external magnetic field to tumor site. Herein, samples were synthesized by using hydrothermal method and characterized by X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), Fourier transform infrared (FTIR), UV–Vis, and Raman spectroscopes. These characterizations confirmed that Fe3O4 nanoparticles have been incorporated between MoS2 nanoflakes successfully. Vibrating sample magnetometer (VSM) was used to see the magnetic characteristics of the samples. This characterization confirmed that the saturation magnetization (Ms) of MoS2–Fe3O4 nanocomposite is enough to separate magnetic nanocomposite quickly from the water sample with an external magnetic field. Finally, photothermal results of samples indicated that nanocomposite produced higher photothermal heat than MoS2 and Fe3O4 individual samples after 10-min laser irradiation (808 nm continuous wave laser, 1 W/cm2). So, MoS2–Fe3O4 nanocomposite can be applied as a suitable photothermal agent for further biological applications such as photothermal therapy, drug delivery, and magnetic resonance imaging (MRI).