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It is the magnetic field topography that determines the ion thruster discharge performance. A three-dimension numerical model of the 20 cm ion thruster discharge chamber was established, and a particle-in-cell method was used to model the discharge process to investigate the effect of the magnetic field topography on the ionization rate and plasma distribution. The results showed that compared with the cylindrical-cusp magnetic field topography, the ring-cusp field made the energetic electrons primarily confined for their increased path length prior to loss to the anode wall and caused the ionization rate to be increased, but the plasma distributed uniformly upstream of the screen grid and the beam flatness was compared to be decreased to 14.8%. When the magnet size was increased and the distance between magnets was changed, the magnetic field contour and the magnetic flux density were modified, and then an improved beam flatness was obtained, from 0.556 to 0.658, by 15.5%.