The low affinity of composite materials for the hard tissue of human teeth poses a challenge to restorative dentists. This study was undertaken to explore molecular and chemical characteristics of the interface between the dental cement, the buffer layer formed from a next generation biomimetic material that mimics the organic mineral composition of human enamel and dentin, and the intact native hard dental tissue. Seven plane-parallel dental slices were analyzed using synchrotron IR microspectroscopy. The obtained absorption spectra of functional molecular groups were organized into cluster maps. This allowed us to identify the intact tissue, the adhesive agent and the biomimetic layer at their interface and to localize and measure concentrations of functional groups involved in the integration of the biomimetic composite into the hard tissue of the human tooth. The proposed biomimetic material is based on nanocrystal carbonate-substituted calcium hydroxyapatite synthesized from a biogenic calcium source and a complex of basic polar amino acids copying the composition of the human tooth and can form a functional bond with hard dental tissue.