The CdZnTe-based and GaAs-based HgCdTe epilayers were grown by liquid phase epitaxy and molecular beam epitaxy, respectively, and then coated by CdTe layers as barrier cap layers for ion implantation. Subsequently, arsenic ions were implanted into the samples at different implant energies, and the two-step high temperature annealing under Hg overpressure was operated on as-implanted samples to eliminate induced damages and activate arsenic ions. After thinning the as-implanted and annealed samples by ion milling, the microstructure of lattice defects in arsenic-implanted and annealed HgCdTe was characterized by high resolution transmission electron microscopy (HRTEM), while the arsenic profiles were measured by secondary ion mass spectroscopy (SIMS). By X-ray diffraction (XRD), the influences of pre-annealing, ion implantation and post-annealing on lattice structure were studied. The experimental results indicate that the implant induced defects underneath the amorphized layer contain dislocation clusters and dislocation lines. For the implant energy of 450keV, a residual point defect belt was observed around the previous amorphous/crystal (a/c) interface in the as-implanted sample after annealing, implying that the recrystallization occurs from surface towards a/c interface. The HRTEM observation of the point defect shows that the defect is a cluster of vacancies in fact. Also, the ion implantation not only broadens the XRD peak, but also makes the peak deviation and split. It indicates that the introduction of atomic stress changes the lattice constant, thereby leading to the peak deviation.