The ion cyclotron resonance (ICR) isotope separation method is an advanced electromagnetic separation method. The key process of this method is the transport of ions in an axial magnetic field. By injecting microwaves at the target ion cyclotron frequency, only the target ions could be heated so that the energy of target ions could be distinguished. Due to the advantages of high separation coefficient, multiple types of isotopes that can be separated, and large throughput, since 1980, countries such as the United States, Russia, and France had already built ICR isotope separation devices and conducted various isotope separation experiments. The main elements of an ICR separation device include three parts: a plasma source, a selective ion heating system, and an ion collector: the electron cyclotron resonance (ECR) ion source is the most popular plasma source, which generates the ions to be separated; the selective ion heating system is the key part of the separation device, mainly composed of a superconducting magnetic coil and a radio frequency (RF) antenna, which are used to provide a stable magnetic field and microwaves at the specific frequency to heating the target isotope ions, respectively; the ion collector is used to collect the ions after separation. To clarify the key process of the ICR separation method, the transport process of ions in the electromagnetic field inside the selective ion heating system is simulated, and the influences on the selective heating effects of core parameters, such as parameters of initial plasma beam and electromagnetic field inside the selective ion heating system, are discussed in detail. The numerical simulation model used in this paper is the single particle model, which ignores the interaction between ions and the induced electromagnetic field of the plasma beam. The simulation results show that the intensity of the alternating electric field in the selective ion heating system, the wavelength of the RF antenna, the size of the ion selective heating system, the initial axial energy of the plasma and its distribution all have a significant impact on the overall heating effect of the plasma beam. The magnetic induction intensity in the ion selective heating system, the wavelength of the RF antenna, and the initial axial energy distribution of the plasma have a direct impact on the selectivity of the heating process. Considering the limitations of the single particle model, further simulation will be conducted using a more accurate model. The design of the RF antenna and ECR ion source will also be considered in the further research.