This paper introduces the basic principle of FDTD algorithm, and the theoretical analysis and formula derivation of FDTD algorithm are carried out. Through modeling the plasma and adopting this algorithm, the mechanism between the electromagnetic wave and plasma will be calculated. Through adopting the MATLAB software to simulate the results, the influences of the plasma frequency，the amount of plasma and collision frequency on the refection characteristics of electromagnetic waves are analyzed. Some important conclusions will be got, and the veracity of results is high compared with the analytical method and WKB method.