The barrier cap layer (BCL) is considered to be able to absorb partially implant induced damages during ion implantation, thus its structure and property could impact the result of ion implantation. In this paper, for As ion implantation in HgCdTe, the different BCLs were deposited on the CdZnTe-based (LPE) and GaAs-based (MBE) HgCdTe epilayers, respectively. Then, the influences of thicknesses and structures of these BCLs on dopant profiles and implant damages were investigated. The as-grown BCLs include thermally evaporated (TE) ZnS, TE CdTe, electron beam evaporated (EBE) CdTe and in-situ CdTe/ZnTe grown by MBE. The SIMS profiles and TEM characterization indicate: For TE ZnS BCLs, there exists an optimized thickness to obtain the deepest As indiffusion after high temperature annealing, and the end-of-range (EOR) depth is linearly proportional to the thickness ratio of a-MCT layer/damage layer. For TE CdTe BCLs, the barrier layer induced channeling effect (BLICE) occurs to the thin BCL samples, while this effect is suppressed in the thick BCL samples. The phenomenon might be due to that the blocking effect of the layered structure inside each crystal column becomes dominate in the thick BCL samples. Additionally, the EBE CdTe BCL with layered structure can suppress effectively the BLICE effect; in the in-situ CdTe/ZnTe BCL, the short defect layer generated in the CdTe buffer layer and the amorphization of the ZnTe layer during ion implantation also play a significant role in suppressing the BLICE effect.