Recent experiments show that the performance of microwave plasma thruster is a little too low because the energy absorbed by plasma depends on the relationship of plasma and microwave frequency. One potential solution is to use external magnetic field to improve the transfer process of microwave in plasma. This paper presents numerical study about how a magnetic field affects the thermal plasma flow field and its temperature in microwave plasma thruster. Out purpose is to see if the magnetic field can enhance the thermal plasma core temperature. Assuming that the plasma within the thruster is under the condition of local thermal equilibrium and the external magnetic fields is uniform, coupled Navier-Stokes, Maxwell and Saha equations are set up to describe the plasma flow under microwave electromagnetic and external magnetic fields. Solving Navier-Stokes equations with semi-implicit method for pressure-linked equations and Maxwell equations with finite-difference time-domain method, the result shows that when the magnetic field intensity is 0.5 T the temperature of plasma core is increased by 24% compared with that at zero magnetic field. Thus the magnetic field improves the performance of microwave plasma thruster.