Chlorhexidine gluconate (CHX) is usually used as a cavity disinfectant in atraumatic restorative treatment, but its remineralized effects on contacted carious dentin are not clear. This research aimed to compare the mean mineral density (MD) difference of carious dentin with or without cavity disinfectant CHX before restoring with high viscosity glass ionomer cement (H-GIC) in vitro. Selective caries removal to leathery dentin was performed in fourteen extracted primary molars with dentin carious lesion. Then, the samples were randomly divided into 2 groups: Group A (n=7) restored with H-GIC (Equia Forte™) without the disinfectant and Group B (n=7) disinfected the cavity with 2% CHX for 1 minute before restored with H-GIC (Equia Forte™). The samples were scanned using microcomputed tomography and analyzed for the mean MD of the teeth at the baseline and after the restoration. The percentages of the mean MD difference between Groups A (Equia Forte™) and B (2% CHX and Equia Forte™) were 14.59 + 9.868 and 30.90 + 14.319, respectively. Group B had a significantly higher percentage of mineral gain than Group A at a 95% confident interval (p-value = 0.029, p-value < 0.05). CHX was shown to inhibit the matrix metalloproteinase (MMP) activity, which can keep collagen cross-linking of tooth structure from collagen degradation. The remineralization of dentin is encouraged from the remaining scaffold collagen fibrils that crystalize minerals. The group with 2% CHX as a cavity disinfectant had higher mean mineral densities gain and percentage of the mean mineral density difference than the non-CHX group. Consequently, 2% CHX enhances the remineralization of adjacent dentin of the restoration.