Currently, natural convection with nanofluid depends on the addition of nanoparticles with a high thermal conductivity to increase the heat transfer performance, often leading to limited increase in heat transfer rate and efficiency. Herein, a magnetically controlled heat transfer method was evaluated. This method enables a rectangular enclosure filled with Fe3O4@CNT nanofluid to achieve controllable heat exchange. Compared with conventional natural convective heat transfer, the magnetically controlled heat transfer method increased the thresholds of heat transfer efficiency by increasing the convective heat transfer. The heat transfer and flow of natural convection can be controlled by the strength and direction of magnetic field. The increase in heat transfer depends on the direction of magnetic field, and the strength of magnetic field determines the degree of heat transfer. This study provides a method to achieve superior convective heat transfer coefficients by controlling the magnetic nanoparticle distribution in a rectangular enclosure.