Anodic oxidation together with hydrothermal treatment has been performed to modify the surface morphology and chemistry of commercial pure titanium (c. p. Ti) and Ti-30Nb-1Fe-1Hf (Ti-Nb) alloy for implant applications. After 6 h of hydrothermal treatment at 250 °C, fine columnar hydroxyapatite (HA) crystals formed on the anodic oxidation film (AOF) of the Ti-Nb plate, whereas coarse columnar HA crystals were observed on the AOF of the c. p. Ti plate. To understand the mechanism of HA formation, the microstructure of the AOF was investigated by cross-sectional TEM. The AOF consisted of three layers, in which the outmost layer comprised nano-crystalline particles dispersed in amorphous oxide matrix. The intermediate layer contained irregular pores, meanwhile the inner barrier layer contacting the substrate was dotted with micro-pores. The amount of Ca and P and the Ca/P ratio decreased gradually from the outer layer to the inner layer of the AOF regardless of the Ti substrate. Nevertheless, the AOF on Ti-Nb had a worse crystallinity than that on c. p. Ti. And, more importantly, this amorphous structure was found to be beneficial for the nucleation of HA crystals during hydrothermal treatment.