A compact crystalline hydroxyapatite coating on Ti-6Al-4V substrate with an atomic intermixed coating/substrate interface about 27 nm in width was synthesized by ion beam assisted deposition (IBAD) and a following post-treatment. The coating after post-treatment was identified by X-ray diffraction as crystalline hydroxyapatite. The interface between coatings and substrates was studied by Auger electron spectroscopy. The adhesive strength between coatings and substrates was measured by scratch tester. The results showed that the adhesive strength of IBAD coatings is nearly twice that of ion beam sputtered coatings. The study also showed that coatings prepared by IBAD eliminated the interfacial deficiencies existing in plasma-sprayed coatings.