Reconstructed layers containing ordered enamel-like structures of fluoride-substituted hydroxyapatite (FHAp) microcrystals were constructed on a human enamel surface using ethylenediaminetetraacetic acid disodium salt dihydrate (EDTA) as the mediating agent under near-physiological conditions (pH 6.00, 37 °C, 1 atm). The effects of initial pH value, fluoride concentration, as well as reaction time on the formation of the FHAp microcrystals, including their microarchitectural structure, crystalline phase, chemical components, and hardness properties, were investigated using transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and Vickers microhardness measurements. The results of these in vitro experiments indicated that EDTA induced the assembly of hexagonal prismlike FHAp microcrystals along their c-axis direction, and the microcrystals further amalgamated with the extended reaction time. In addition, fluoride ions were found to play a critical role in the formation of hexagonal FHAp microcrystals. Interestingly, after reaction for 5 days, the Vickers microhardness of the new layer (347–370 VHN) was harder than that of natural tooth. On the basis of the experimental evidence, a mesoscale self-assembly mechanism was proposed to explain the growth of FHAp microcrystals.