In magnetic field design principle of microwave discharge ion thruster, it is universally received that enlarging the magnetic mirror region can confine more electrons to acquire better energy utilization rate, while reducing the magnetic field diffusion region can prevent electrons from losing at wall to reduce the discharge loss. However, recently the integrated simulation proposes a hypothesis that electrons can also be heated in the magnetic field diffusion region when the Child-Langmuir sheath is considered as a constraint condition for electrons. Therefore, herein a magnetic field structure for the magnet array microwave discharge ion thruster is designed to verify the hypothesis, in which the magnetic field diffusion region is located near the screen grid. Then, an integrated simulation is conducted for studying the initial discharge and ion beam extraction stages of the thruster. The simulation results show that in the magnetic field diffusion region, the electron temperature is 4–8 eV when the grid system voltage is not applied, while the electron temperature is 4–12 eV when the the grid system voltage is applied. And the plasma density in the latter case has one order of magnitude higher than that in the former case. It means that electrons are obviously heated in the magnetic field diffusion region when they are confined among the Child-Langmuir sheath, the plasma sheath at antenna surface, and magnetic mirror. This electron heating mode produces more high-energy electrons outside the magnetic mirror region to generate plasma in front of the grid system, which can significantly increase the plasma density and ion beam current density. The result shows that under the conditions of 0.3 sccm (1 sccm = 1 mL/min) xenon gas flow, 1 W input microwave power, 300 V screen grid voltage and –50 V acceleration grid voltage, the ion beam current and its density are 0.47 mA and 0.60 mA/cm ²for the magnet array microwave discharge ion thruster, while the ion beam current and its density are 1.2 mA and 0.38 mA/cm ²for the 2-cm microwave discharge ion thruster. The ion beam current density increases by 57.9%. Through the integrated simulation, a new electron heating mode in the magnetic field diffusion region is proved theoretically, which provides a theoretical basis for the magnetic field structure optimization of microwave discharge ion thruster.