© 2016 American Chemical Society. To clarify hydroxyapatite (HAp) nanocrystal formation based on the interfacial interactions with organic molecules is important for controlling the dispersion states/shapes of HAp and understanding the biomineralization mechanism. In this study, the effects of cetyltrimethylammonium bromide (CTAB) micelles on the HAp nanocrystal formation process were investigated through both the morphosynthesis technique and the molecular orbital calculations. The HAp nanocrystals synthesized in the presence of CTAB exhibited a controlled rod-like shape and subsequently grew up by a thermal treatment to be larger-sized nanocrystals at a well-dispersed state. It was also found that the CTAB micelles strained and disordered at the higher temperature effectively induced heterogeneous nucleation to initiate the nucleation/growth processes. In contrast, HAp nanocrystals synthesized without CTAB exhibited irregular-shaped and aggregated nanocrystals, which are due to dominantly occurring homogeneous nucleation. According to the molecular orbital calculations, the cationic N atom of the CTAB molecule strongly interacted with the Ca ion in the a-plane as well as the hydroxyl/phosphate groups in the c-plane of HAp via ionic/covalent bonding (e.g., only ionic bonding at the closer interfacial distance at 1.0 Å), leading to effective nucleation on the micelle surfaces. Therefore, a possible reason for the rod-like and well-dispersed nanocrystal formation is due to the heterogeneous nuclei formation/growth on the N atoms of CTAB micelles and subsequent fusion growth among the CTAB micelle-directed inorganic-organic complexes in the confined spaces. The present results will be applicable for designing tailored HAp morphologies based on inorganic-organic hybrid interaction systems.