The present work introduces combination of superparamagnetic iron oxides (SPIONs) and hexamolybdenum cluster ([{Mo6I8}I6]2−) units within amino-decorated silica nanoparticles (SNs) as promising design of the hybrid SNs as efficient cellular contrast and therapeutic agents. The heating generated by SNs doped with SPIONs (Fe3O4@SNs) under alternating magnetic field is characterized by high specific absorption rate (SAR = 446 W/g). The cluster units deposition onto both Fe3O4@SNs and “empty” silica nanoparticles (SNs) results in Fe3O4@SNs[{Mo6I8}I6] and SNs[{Mo6I8}I6] with red cluster-centered luminescence and ability to generate reactive oxygen species (ROS) under the irradiation. The monitoring of spin-trapped ROS by ESR spectroscopy technique indicates that the ROS-generation decreases in time for SNs[{Mo6I8}I6] and [{Mo6I8}I6]2− in aqueous solutions, while it remains constant for Fe3O4@SNs[{Mo6I8}I6]. The cytotoxicity is low for both Fe3O4@SNs[{Mo6I8}I6] and SNs[{Mo6I8}I6], while the flow cytometry indicates preferable cellular uptake of the former versus the latter type of the nanoparticles. Moreover, entering into nucleus along with cytoplasm differentiates the intracellular distribution of Fe3O4@SNs[{Mo6I8}I6] from that of SNs[{Mo6I8}I6], which remain in the cell cytoplasm only. The exceptional behavior of Fe3O4@SNs[{Mo6I8}I6] is explained by residual amounts of iron ions at the silica surface