Due to the multiple factors contributing to dentin demineralization and hypersensitivity among individuals, the effectiveness of the available treatments in the long term remains unclear. A recent study reported a simple strategy to potentially mimic natural remineralization with increased crystallization on the enamel caries using fluoride iontophoresis. Such an effect is also ideal for accomplishing dentin biomineralization and structural strength. This study aimed to investigate structural and compositional characteristics and permeability changes after fluoride iontophoresis with different polarities, cathodal iontophoresis (CIP), anodal iontophoresis (AIP), and the control without iontophoresis for the treatment of etched dentin under simulated pulpal pressure. The 24 premolars were divided into 3 groups: CIP, AIP, and topical application of 5% sodium fluoride (NaF) for 40 s. Relative to before treatment, iontophoresis with both polarities significantly decreased the permeability with a visible increase in occluding tubules containing crystal formation and growth throughout the dentin structure and depth. The CIP not only restored the etched dentin surface into a sound condition but also reinforced the dentin across the structure and depth by the synergistic effects of remineralization, increasing crystal formation and transformation toward the more crystalline structure of fluorohydroxyapatite. Following topical treatment, X-ray diffraction analysis and Raman spectra revealed a significant reduction in the crystal size and crystallinity associated with the raised B-type carbonate substitution into the hydroxyapatite compared with that in the sound dentin. The result was the first to reveal the ideal strategy to rapidly restore the etched dentin surface into a sound condition, including reinforcing the dentin across the structure and depth by the synergistic effects of decreasing permeability, increasing crystal formation, and transformation toward the more crystalline structure of fluorohydroxyapatite using the 5% NaF applied with the DC cathode iontophoresis. The technique is noninvasive and simple and deserves further development for clinical application.