The penetrating defects of HgCdTe by liquid phase epitaxy (LPE) can lead to the formation of multiple blind elements in subsequent device preparation. The depth of this type of defect was characterized using confocal microscopy, and the composition of the bottom of the defects was tested. The defects were dug up using a focused ion beam (FIB) and observed. For HgCdTe thin films on CdZnTe substrates with more penetrating defects, it was found that there is a certain correspondence between the penetrating defects on the surface of HgCdTe and the substrate defects. Therefore, it is speculated that the penetrating defects of HgCdTe by LPE originate from CdZnTe substrate defects.