One of the most common systems for bone tissue engineering is polymeric scaffolds. However, the low mechanical properties of polymeric scaffolds, considering the properties required for bone replacement tissue, are the main challenge for researchers in this field. For bone tissue engineering, this research prepared nanocomposite scaffolds based on polyvinyl alcohol-chitosan containing modified clay and hydroxyapatite (HAp). HAp used in these 3D scaffolds was synthesized from a chicken femur, and Cloisite 30B clay nanoparticles were modified by graphene oxide and Fe3O4 nanoparticles to strengthen their mechanical properties. Sample characteristics were determined using FT-IR, XRD, SEM, TGA, swelling rate, laboratory degradation, and biological and mechanical properties. These analyses showed that 2% of modified clay (C30B/GO/Fe3O4, CGF) inside the nanocomposite scaffold increased the compressive strength 23 times compared to the pristine polymer scaffold. Also, adding HAp particles and modified clay simultaneously increased the mineralization on the surface of the scaffolds. Final nanocomposite scaffolds were found to have a compressive strength of 9.31 MPa, a porosity of 75 %, and a porosity size of 50 nm and were in the range of cancellous bone. The final swelling amount is 1790 %, which is the amount that is Favorable for bone scaffold. Finally, the analysis results to determine the samples' toxicity showed that none of the prepared scaffolds were toxic and showed good cell viability.