Influence of Hg vapor to CZT substrate during LPE growth of HgCdTe process were studied, CZT substrates were characterized by combining with Microscope, White-light Interferometer (WLI) and Energy Dispersive Spectrometer (EDS) . Results show that the CZT substrates mainly suffered the Hg vapor during LPE process，Hg vapor has no effect on the precipitations in CZT substrates surface. Two kinds of typical Hg erosion defects are found on CZT substrates after Hg vapor treatment process. One is a kind of large defect that had size of 25 μm and distributed uniformly, while the other is smaller size of 7 μm presented nonuniform distribution. Furthermore, fish scale like surface morphology on CZT substrate is found after Hg vapor treatment process during LPE growth of HgCdTe, surface roughness increase more than 50%.