Based on graphical processing unit acceleration, a new method of finite-difference time-domain scheme is proposed to simulate the interaction between electromagnetic waves and magnetized plasma in two-dimensional conditions. In this study, transversely electric and transversely magnetic are computed in time to avoid matrix operations involving Lorentz equations of motion. Compared to Young’s method, the new method reduces addition and multiplication by about 63% and 66%, respectively. The simulation results of ionospheric wave propagation show that the new method agrees well with Young’s method and the calculation speed is improved significantly.