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The xenogeneic decellularized corneal matrix (DCM) was expected to be used in lamellar keratoplasty in clinic as the substitute of allogeneic cornea. After decellularization treatment, the remaining risk of xenograft rejection needed to be assessed. The galactose-α1,3-galactose, as the most abundant and closely rejection-related xenogeneic antigen, should be one of the important factors concerned in immunological evaluation. In this study, residual αGal in the DCM was first determined by an enzyme-linked immunosorbent assay method with qualified accuracy and specificity. Then the DCM was implanted subcutaneously into the α1,3-galactosyltransferase gene-knockout (GTKO) mice, accompanied by the implantation in the wild-type C57BL/6 mice as a comparison. The total serum antibody levels, anti-Gal antibody levels, inflammatory cytokines and ratios of splenic lymphocyte subtypes were detected and the histopathological analysis of implants were performed to systematically evaluate the immune responses. The experimental result showed the fresh porcine corneal matrix samples had (9.90 ± 1.54) × 1012αGal epitope per mg while the content of residual αGal in the DCM was (7.90 ± 2.00) × 1012epitope per mg. The GTKO mice had similar potential of reaction to immune stimulation to that of wild-type C57BL/6 mice. At 4 weeks after implantation of DCM, in WT mice and GTKO mice there were both innate immunity response to the DCM characterized by macrophage infiltration. But the elevations of anti-Gal IgG level and the percentage of splenic natural killer cells were only detected in GTKO mice. These changes were thought to be pertinent to the residual αGal antigen, which could not be detected in WT mice. No further αGal antibody-mediated cellular immunity and significant changes of serum cytokine contents were found in GTKO mice, which perhaps suggested that the immune reactions to the DCM after 4 weeks of implantation were moderate and had minor effect on the survival of the corneal graft.