The gold (Au) nanoparticles (NPs) with the diameter of 15–40 nm were successfully synthesized in the hierarchical hydroxyapatite (HAp) nanostructures of natural fish scale templates, which were carried out by the Au3+ ion chemisorption, reduction and calcination processes to form the AuNPs/HAp hybrids. The AuNPs size as well as the surface plasmon resonance (SPR) absorption maximum was preserved with the hybridization process. Moreover, the AuNPs/HAp hybrid nanostructures exhibited preferential protein adsorption behavior at the biological bovine serum albumin (Ab) concentration regions that correspond to be 1.5 μM in the cell culture medium and 15.1 μM in human blood, and the Ab adsorption equilibrium constant of AuNPs/HAp hybrid was higher than that of the HAp alone. The SPR absorption maxima of the Ab-adsorbed AuNPs/HAp fish scales were red-shifted as compared with those of the AuNPs/HAp fish scales. Therefore, we synthesized the AuNPs using the fish scale template to exhibit the preferential protein adsorption, which will be a great significance to research the AuNPs/HAp hybrid functions.