HgCdTe is a well-known material for state-of-the-art infrared photodetectors. The interd-iffused multilayer process (IMP) is used for Metal–Organic Chemical Vapor Deposition (MOCVD) of HgCdTe heterostructures, enabling precise control of composition. In this method, alternating HgTe and CdTe layers are deposited, and they homogenize during growth due to interdiffusion, resulting in a near-uniform material. However, the relatively low (350 °C) IMP MOCVD growth temperature may result in significant residual compositional inhomogeneities. In this work, we have investigated the residual inhomogeneities in the IMP-grown HgCdTe layers and their influence on material properties. Significant IMP growth-related oscillations of composition have been revealed in as-grown epilayers with the use of a high-resolution Secondary Ion Mass Spectroscopy (SIMS). The oscillations can be minimized with post-growth annealing of the layers at a temperature exceeding that of growth. The electric and photoelectric characterizations showed a significant reduction in the background doping and an increase in the recombination time, which resulted in dramatic improvement of the spectral responsivity of photoconductors.