It was developed that finite-difference time-domain(FDTD) method is applied to photon scanning tunneling microscope(PSTM).A novel method "three-wave method" in specifying the incident wave throughout the problem space in PSTM,which includes the incident wave,reflective wave and transmitted evanescent wave,was proposed.The difficulty that threre are the substrate and total internal reflection wave in the problem space was solved applying FDTD in PSTM.We show the physical pictures about the interaction between the probe tip and sample and photon tunneling effect in PSTM.And we simulated the scanning process when the probe tip scan above the sample in constant-height mode.The images of PSTM were presented.At last,we compared the scanning curves in constant-height mode in the condition of single light beam and two light beams illuminated respectively,and the former has some shift,the latter the shift can be corrected.