Objective:The purpose of this study were to compare mean mineral density(MMD) and examine the remineralized pattern of carious dentin after cavity disinfectant with chlorhexidine gluconate (CHX) and restore with H-GIC in vitro. Materials and Methods: Selective caries removal to leathery dentin was performed in forty extracted primary molars. The samples were scanned using micro-computed tomography (micro-CT) as the MMD baseline and randomly divided into 4 groups: Group A (n=10) applied dentin conditioner and restored with H-GIC (Equia Forte™), Group B (n=10) disinfected the cavity with 2% CHX for 1 minute before applied dentin conditioner and restored with H-GIC (Equia Forte™), Group C (n=10) restored with H-GIC (Ketac Universal™) and Group D (n=10) disinfected the cavity with 2% CHX for 1 minute before restored with H-GIC (Ketac Universal™). After restoration, all samples were scanned micro-CT as the MMD after restoration. All samples were subjected to pH cycling process for 14 days and scanned micro-CT as the MMD after pH cycling. One sample from each group was randomly selected to analyze by the scanned electron microscope (SEM). Results: The comparison of MMD gain after restoration among 4 groups was a significant difference between EquiaTM and CHX-KetacTM group (oneway ANOVA with Post hoc (Tukey) test, P = 0.045). Group A: the MMD gain after restoration (±SD) was 88.81 (±59.857), group B; 168.29 (±100.899), group C; 165.54 (±72.366) and group D; 183.00 (±73.096) mgHA/ccm. Moreover, there was a significant difference of the MMD gain after restoration between EquiaTM and CHX-EquiaTM group (Independent t-test, P = 0.046). But between KetacTM and CHX-KetacTM group, there was no difference. From SEM, CHX-KetacTM group had the smallest dentinal tubule orifices and the thickest intertubular dentin among 4 groups. CHX-EquiaTM group had thicker intertubular dentin than EquiaTM group. Conclusion: The groups with 2% CHX as a cavity disinfectant had higher MMD gain and thicker intertubular dentin than non-CHX group. Therefore, the application of 2% CHX on demineralization dentin enhances the remineralization of contacted dentin underneath the restoration.