In the preparation of a hydroxyapatite [HAp]/gelatin [GEL] nanocomposite, the GEL matrix in aqueous solution of $H_3PO_4$ was modified by the introduction of aspartic acid [Asp], asparagine [Asn], and glycine [Gly]. The addition of Asp, Asn and Gly greatly affected the slurry formation of HAp/GEL nanocomposite and the resulting dry body showed variations in toughness with the addition of the different amino acids. The introduction of Asn into HAp/GEL nanocomposite was effective for producing the organic-inorganic interaction between HAp and GEL, and caused the increase of toughness. The formation reaction of the modified HAP/GEL nanocomposites was investigated by using XRD and FT-IR. The organic-organic interaction between the GEL matrix and the additives of Asp, Asn and Gly was confirmed from FT-IR analysis, and the organic-inorganic interaction between HAp nanocrystallites and the modified GEL matrix was also discussed, using FT-IR spectra patterns. Nanocrystallites of HAp were covalently bound with the GEL macromolecules and differently influenced by the modification species of Asp, Asn, and Gly.