Aiming at improving the capture performance of inner vortex electrostatic cyclone (ESC), which is widely used in the field of flue gas purification, magnetic field is introduced to remove submicron particles. The theoretical and physical models of electromagnetic dust removal were established, and the dust-removal efficiency of submicron particles under different temperatures and magnetic fields was numerically simulated by FLUENT. The results show that a rise in temperature leads to a reduction in the grade efficiency of submicron particles of ESC, a decrease in the number of escaped particles at lower temperature, and the differences of the rising amplitude in overall efficiency corresponding to the traditional cyclone, which were 36.7%, 34.8%, 33.8%, and 31.9% at four temperatures. The contribution of temperature to the capture of submicron particles decreases continuously with the increasing temperature, but that of magnetic field progressively increases at this time. The magnetic field environment is conducive to the capture of submicron particles, the removal effect is more obvious with the increase of magnetic flux density, but the ascended ranges of magnetic field and temperature both decrease when it reaches 0.5 T. These results can provide a theoretical basis and a technical reference for the design of ESC.