Hydroxyapatite (HA) is a significant constituent of bones or teeth and is widely used as an artificial bone graft. It is often used to replace the lost bones or in reconstructing alveolar bones before dental implantation. HA with biological functions finds its importance in orthopedic surgery and dentistry to increase the local concentration of calcium ions, which activate the growth and differentiation of mesenchymal stem cells (MSC). To make relevant use of HA in bone transplantation, the surfaces of orthopedic and dental implants are frequently coated with nanosized hydroxyapatite (nHA), but its low dispersibility and tendency to form aggregates, the purpose of the surface modification of bone implants is defeated. To overcome these drawbacks and to improve the histocompatibility of bone implants or to use nHA in therapeutic applications of implants in the treatment of bone diseases, various studies suggested the attachment of biomolecules (growth factors) or drugs through chemical bonding at the surface of nHA. The growth factors or drugs bonded physically at the surface of nHA are mostly unstable and burst released immediately. Therefore, reported studies suggested that the surface of nHA needs to be modified through the chemical bonding of biologically active molecules at the surface of bone implants such as proteins, peptides, or naturally occurring polysaccharides to prevent the aggregation of nHA and to get homogenous dispersion of nHA in solution. The role of irradiation in producing bioactive and antibacterial nHA through morphological variations in surfaces of nHA is also summarized by considering internal structures and the formation of reactive oxygen species on irradiation. This mini-review aims to highlight the importance of small molecules such as proteins, peptides, drugs, and photocatalysts in surface property modification of nHA to achieve stable, bioactive, and antibacterial nHA to act as artificial bone implants (scaffolds) in combination with biodegradable polymers.