Many photothermal materials have been developed in recent years to achieve efficient photothermal therapy. Although larger-sized materials are preferred to ensure a better photothermal performance, upsizing hampers the cellular uptake of these materials. To overcome this dilemma, we proposed an active control system to manipulate the assembly of magnetic composite particles (MCPs) at the cellular level. Herein, MCPs of different sizes (small, medium, and large) were synthesized, and their surfaces were modified with a polymer. These MCPs were then cultured with HeLa cells, and their uptake and mobility were investigated. Small-sized MCPs (d v = 206 nm) and medium-sized MCPs (d v = 312 nm) could be introduced into HeLa cells. However, a smaller amount of the large-sized MCPs was introduced as compared to the other MCPs. Using a direct current magnetic field [DCMF (B = 150 mT)], medium-sized MCPs were observed to quickly assemble in cells; however, redispersal did not occur after the DCMF was turned off. To improve the particle dispersibility, polyethylene glycol and polyethyleneimine (PEI) were used to modify the medium-sized MCPs. Coating the MCPs with PEI (a polymer molecular weight of 25,000 or 270,000) improved their dispersibility in phosphate-buffered saline and cellular uptake. In addition, the redispersal of assembled PEI-coated MCPs was observed after the DCMF was turned off. The photothermal conversion efficiency of the MCPs was also improved using the DCMF. Consequently, the PEI-coated MCPs were first introduced into cells in a dispersed state, and their assembly was induced at the subcellular scale by applying a DCMF, and the assembly was spontaneously redispersed by switching off the DCMF. Such a remote control could improve the cytotoxicity of MCPs under near-infrared laser irradiation.