Hydroxyapatite (HAp) nanoparticles-based miRNA delivery system has emerged as a promising therapeutic agent for bone regeneration application. In order to achieve high therapeutic performance, the development of HAp functions remains challenging. This study describes the influence of HAp characters on their biological activities with osteoblast cell by synthesized different sizes of rod-like HAp with 150-200 and 100 nm in size and the different shape of elongated particles with 100-150 nm in size. A comparison was carried out on cytotoxicity, cellular uptake, and miRNA binding capacities. The elongated and rod-like shapes of 100-150 nm illustrated the high cell viability, and interestingly, the highest cellular uptake efficiency was observed in elongated particle. However, both particles revealed low ability to condense with miRNA due to their negative surface, the cationic functional molecules, which are APTES and PDMAEMA, were modified on the elongated particle to investigate how surface charge affect their biological properties. The biocompatibility, as well as the high cellular uptake and high miRNA loading efficacies, were noticed in HAp/APTES nanoparticle, which made it possible to be an efficient carrier system for miRNA therapy application. The obtained results could demonstrate a starting point for the development of a HAp-based miRNA delivery system using in bone regeneration application.