To minimize the impact of defects in mercury cadmium telluride (MCT) thin films grown by liquid phase epitaxy (LPE) on infrared detector performance, a special surface defect (the frustum-shaped defect) is systematically studied using a variety of characterization methods, including scanning electron microscope (SEM), energy-dispersive X-ray spectrometer (EDX), and focused ion beam (FIB), combined with comparative experiments. These defects range in size from 150 μm to 400 μm and appear as a concave frustum-shaped morphology under an optical microscope. Compositional analysis reveals no significant differences in composition between the defect surface and the film surface without defects. Analysis of the interface between the cadmium zinc telluride (CZT) substrate and the MCT epitaxial layer confirms that the defect is a through-hole defect, originating from triangular tellurium inclusions with holes in the center of the CZT substrate. The tellurium inclusions are almost always larger than 20 μm in size. Therefore, by improving the quality of the CZT substrate and optimizing the substrate screening process, it is possible to effectively reduce the frustum-shaped defects in MCT thin films, improve the quality of the epitaxial material, and meet the development needs of high-performance infrared detectors.