In this paper, the limitations of two-dimensional magnetic field configuration for an annular ion thruster are analyzed theoretically and numerically. The two-dimensional magnetic field, which is commonly used in traditional ion thrusters, has been proved to be a very effective way for the confinement of primary electrons and ions. Hence, the confinement characteristics of primary electrons and ions in an annular ion thruster with the two-dimensional magnetic field configuration are first analyzed theoretically. Then, according to the analysis, a two-dimensional magnetic field for an annular ion thruster is designed. On this basis, the limitations of the two-dimensional magnetic field configuration are analyzed and discussed by a three-dimensional (3D) Particle-in-cell Monte Carlo collision (PIC-MCC) model. The results show that if the collision process is not considered, a uniform distribution of primary electrons can be achieved theoretically. However, when considering the collision process, the atom forms a significant impedance to the circumferential motion of primary electrons, thus greatly increasing the loss rate of primary electrons. Finally, it is found that, since primary electrons are not guided and constrained in the circumferential direction under the two-dimensional magnetic field, the discharge uniformity cannot be improved only by increasing the magnetic field intensity.