The results are based on the first principal modeling and calculations for hydroxyapatite (HAP) nanostructures as native as well surface modified, charged and having various defects (H and OH vacancies, H internodes). HAP structures having being studied using Local Density Approximation (LDA) method with calculations of Density of States (DOS) allow us analyzing the experimental forbidden energy gap (Eg) and work function data. Molecular modeling by HyperChem is confirmed by photoelectron monochromatic measurements up to 6 eV and photoluminescence (PL) data from synchrotron DESY experimental data up to 30 eV values. Brief analysis of the influence of heating, microwave radiation, hydrogenation, x-rays and synchrotron radiation on HAP surface is presented in this work. New data of the structure of modified hydroxyapatite are obtained. The determined energy levels for H internodes is EH-int ~ Ev + (1.5–2.0) eV, while for OH vacancy energy is in the range of EOH-vac ~ Ev ~ Ev + (2.9–3.4) eV inside the forbidden zone Eg. The analysis of PL emission allows us to conclude that these energies are close to observed main PL spectral line 420 nm (2.95 eV), and consequently OH vacancy could play the leading role in the surface energy levels changes and charging. But the influence of the inserted hydrogen is revealed too through excitation from most deep valence band levels due to existence of close overlapped molecular orbital with phosphorus atoms in the excited states. Both defects are observed by PL emission spectrum under synchrotron excitation energy in diapason ~8.5–14.5 eV.