The microstructure and inhomogeneous features of plasma-sprayed hydroxyapatite coatings on titanium substrates have been examined using the time-of-flight secondary ion mass spectroscopy (ToF-SIMS), micro-Raman spectroscopy and nano-indentation techniques. The crystalline and amorphous areas in coatings can be identified by the elastic modulus difference. The concentration gradient of O and OH ions was detected in the through-thickness direction of coatings. Lack of O and OH ions near the titanium interface implies the existence of phases other than HA, and might result in excessive adsorption of the coatings near the interface in HA-coated Ti implants.