The influence of heterogeneous microstructures on the anodization behavior and biocompatibility of Ti-based alloys was investigated. A heterogeneous Ti-15Zr alloy was fabricated by powder metallurgy, followed by hot rolling and heat treatments. Electrochemical anodization was then applied to obtaining a nanotube-arrayed surface. The results show that the surface of the anodized heterogeneous Ti-15Zr alloy consists of nano-sized tube structure as well as micron-scaled tubular clusters and microcracks. The formation of such a surface should be attributed to the (0001)-oriented striped grains and the heterogeneous Zr distribution. Compared with the anodized arc-melted Ti-15Zr control group, the anodized heterogeneous Ti-15Zr exhibits comparable super-hydrophilicity, better protein adsorption, and improved cell proliferation, mainly due to the hierarchical surface structures of the latter.