HgCdTe films grown by molecular beam epitaxy (MBE) are essential for creating high-performance infrared focal plane arrays (IRFPAs) like dual band detectors, high operating temperature (HOT) detectors, and avalanche photodiode (APD) detectors. CdZnTe is recognized as the optimal substrates for growing high crystal quality HgCdTe due to its lattice matching, which is adjusted by selecting the Zn mole fraction. However, defects like grain boundaries, twins, inclusions, dislocations, and sub-grain boundaries that often occur in CdZnTe substrates can significantly reduce the crystal quality of HgCdTe. HgCdTe grown on CdZnTe with these defects usually no longer suit for high quality device fabrication. Although the impact from various defects have been extensively studied in HgCdTe grown on CdZnTe, but the sub-grain boundaries is still not yet involved. In our study, to better understand the effect of sub-grain boundaries in CdZnTe on HgCdTe films, CdZnTe substrates with and without sub-grain boundary were selected to growth MWIR HgCdTe films under optimized condition. Results indicated that etch pit density (EPD) of CdZnTe substrates with sub-grain boundary is approximately 3–5 times higher than boundary free areas. But HgCdTe grown on these substrates bears more than an order of magnitude increase in dislocation proliferation compared to the boundary free region. Dislocation generation resulting from dislocation penetration from substrates, mismatch between HgCdTe and CdZnTe, and sub-grain boundaries were investigated and compared. The intense dislocation proliferation in HgCdTe may be mainly due to twins formed during the initial growth stage of HgCdTe films, rather than dislocation penetration from substrates, as revealed by reflection high-energy electron diffraction (RHEED) pattern monitoring. Therefore, screening for sub-grain boundaries in CdZnTe before HgCdTe growth is necessary.