How the surface topography of hydroxyapatite (HAP) coatings remodels hard tissue is of utmost importance and a contributing factor to ambiguity regarding this subject. Here, HAP coatings with different topographies of a rod-like nanoarray with c-axis orientation and a flake-like micro-flower array with a(b)-axis orientation on a Ti substrate were synthesized via hydrothermal-electrodeposition by controlling the concentration of electrolytes. XRD, TEM and SAED analyses indicated that the rod-like HAP nanoarray was predominant with an orientation of (001), while the HAP micro-flower samples were based on an orientation of (100). Compared to the flake-like HAP, the rod-like nanoarray HAP possessed better hydrophilic properties and lower roughness, which not only enhanced adsorption of specific fibronectin proteins but also promoted the spreading and growth of MC3T3-E1 cells. Runx2, alkaline phosphatase, collagen and osteocalcin were also analyzed by RT-PCR on the two distinctive HAP-coated samples. MC3T3-E1 cells on the rod-like nanoarray coating had higher osteo-related gene expression. This finding suggested that the ordered assembly structure of the HAP might cause topography-dependent coordination with biomolecules for enhancing osteoblast-like cell proliferation and osteogenic differentiation. This study provided an understanding of the surface's features for biomaterials to ensure better bioactivity.