Deamination is a method used to modify the physicochemical and nutritional properties of proteins. Here the effect of deamination using an acid method on the in vitro digestibility of rice, wheat, and corn proteins was studied. Additionally, the mechanism underlying the effects of the deamination on the in vitro digestibility of proteins in three types of grains was explored in terms of physicochemical properties including solubility, surface hydrophobicity, sulfhydryl and disulfide content, and ultrastructure. The results showed that with an increasing degree of deamination, the difference in the inter-conversion between sulfhydryl and disulfides in the proteins of the three types of grains (rice, wheat, and corn) was not significant (p < 0.05), and the sulfhydryl and disulfide contents were generally unchanged. Protein solubility in the three types of grains at the optimum pH for pepsin (pH = 1.5) and trypsin (pH = 7.5) was slightly increased; however, surface hydrophobicity slightly decreased with an increasing degree of deamination. The in vitro digestibility of rice, wheat, and corn proteins increased from 66.5% to 79.5%, 79.5% to 89.0%, and 78.5% to 89.2%, respectively. Meanwhile, the protein ultrastructure, which was originally dense and compact, became porous and loose, which was more conducive to digestion.