The Finite Difference Time Domain(FDTD) method is adopted to study the transmission characteristics of microstrip structure, and a novel method is proposed to improve the efficiency of S-parameter computation. The Input impedance Zin of the system can be obtained by recording the current and voltage values of reference points. According to transmission line theory, the relationship between reflection coefficient S11 and the transfer impedance Zin can be built. And an expression for the relationship between Sn1 and Zin of n-port network is obtained by further studying.The method avoids a problem of separating the incident and reflect waves when using FDTD, which makes the model more compact, saves the computer memory, and reduces the complexity of programming.