The aim of this article was to evaluate the effects of modifying glass ionomer cement (GIC) with carboxymethyl chitosan (CMC) on surface morphology and remineralization outcomes by examining dentin morphology and calcium ion composition changes. Thirty holes in a cylindrical acrylic mold were filled with three groups of restorative materials: GIC, GIC modified with CMC (GIC-CMC) 5%, and GIC-CMC10%. The surface morphology of each group's materials was observed using scanning electron microscopy (SEM). The compressive strength measurement was performed using a universal testing machine. The dentin remineralization process was performed by applying GIC, GIC-CMC5%, and GIC-CMC10% materials for 14 days on demineralized dentin cavities treated with 17% ethylenediamine tetraacetic acid (EDTA) for 7 days. A morphological evaluation was conducted using SEM. The calcium ion composition and calcium-to-phosphorous (Ca/P) ratio were examined using an energy-dispersive X-ray (EDX). The Kruskal-Wallis and post-hoc Mann-Whitney U tests were performed to compare all four groups of calcium ions (p < 0.05). The modification of GIC with CMC affected the morphological changes in the materials in the form of reduced porosity and increased fractures. A significant difference was found in compressive strength between the GIC-CMC modification materials of GIC-CMC5% and GIC-CMC10% and the GIC control group. The dentin tubule morphology and surface changes were observed after applying GIC, GIC-CMC5%, and GIC-CMC10% materials for 14 days, as evaluated by SEM. The EDX examination showed an increase in calcium ion content and hydroxyapatite formation (Ca/P ratio) after applying the GIC-CMC10% material. The surface porosity of the GIC modification material with the addition of CMC tended to decrease. However, an increase in cracked surfaces that widened, along with the rise in CMC percentage, was found. This modification also reduced the compressive strength of the materials, with the lowest average yield at 10% CMC addition. Therefore, the modification of GIC with CMC affects changes in morphology, calcium ion composition, and Ca/P ratio in demineralized dentin.