In this study, gelatin-hydroxyapatite (GEL/HA) composites as biological organic-inorganic composites were made up of the capability for use in hard tissue to be examined by two methods, direct mixing and biomimetic. In the direct mixing method, after the synthesis of hydroxyapatite, the resulting powder was mixed with gelatin; in the biomimetic method, hydroxyapatite was synthesized in the presence of gelatin. The thin layer composite substrates were prepared with a thickness of 2 mm from the resulting mixture by combining methods including casting solvent and freeze-drying. The three-dimensional scaffolds were modified by glutaraldehyde as a crosslinked factor. The results showed that scaffolds have a high porosity of approximately 88% and are interconnected with holes. According to the SEM image, the average pore size is around 100 μm. A study of Infrared spectroscopy (FT-IR) and X-ray diffraction (XRD) indicated that the apatite phase formation non-stoichiometric low crystalline along with extensive replacement of carbonate ions on the network that is very biologically close to apatite phase and two composite components not only physically but also chemically interact with each other. Compressive strength test results also show that both scaffolds have mechanical properties similar to the cancellous bone. Young's modulus and density increase, and porosity and water absorption decrease by increasing the content of the hydroxyapatite composite. Despite the suitability of both methods, it seems that the biomimetic-made scaffolds are more suitable due to the higher density, higher tolerance levels of stress and Young's modulus, lower crystallinity, and replacement of carbonate ions appropriate method.