Nanotopographic modification is one of the effective strategies to guide cell behaviors and improve the bioactivity of biomaterials. Hydrothermal synthesis has been preferably used to produce low-dimensional nanostructured materials due to its simplicity, cost-effectiveness and controllability of crystal morphologies. However, assembling low dimensional nanosized units into an integrated and well-ordered high dimensional structure (2D film and 3D architecture) on biomaterials or biomedical devices remains a big challenge. In this study, we designed a novel substrate-dependent hydrothermal strategy to produce a biocompatible hydroxyapatite (HAp) nanorod array structure and well-organized nano-sheet architecture on a HAp–tricalcium phosphate (TCP) bioceramic – one of the widely used biomaterials in bone tissue engineering. The nanorod array structure resulted from the “nanocarving” process in the reaction with buffered solutions, while the well-organized nano-sheet architecture was formed by the subsequent mineralization deposition on the nanorod array structure. Both “nanocarving” and mineralization deposition processes are strongly dependent on the phase composition of the HAp–TCP substrates and influenced by the Ca and P ion concentrations of the buffer used. Compared to the conventional surface of the as-sintered ceramics, nano-sheet architecture promoted primary human osteoblast (HOB) adhesion as reflected by the activation of focal adhesion kinase (FAK) and expression of actin in HOBs. In summary, our study provided a simple solution based approach to endow HAp–TCP bioceramics with more favorable topographical features compared to the conventional ceramic surface.