The role of scaffolds in bone regeneration is of great importance. Here, the electrospun scaffolds of poly (3-hydroxybutyrate)-keratin (PHB-K)/nanohydroxyapatite (nHA) with different morphologies (long nanorods (HAR) and very short nanorods (HAP)) and weight percentages (up to 10 w/w%) of nHA were fabricated and characterized. The fibers integrity, the porosity of above 80%, and increase in pore size up to 16 μm were observed by adding nHA. The nanofibers crystallinity increased by 13.5 and 22.8% after the addition of HAR and HAP, respectively. The scaffolds contact angle decreased by almost 20° and 40° after adding 2.5 w/w% HAR and HAP, respectively. The tensile strength of the scaffolds increased from 2.99 ± 0.3 MPa for PHB-K to 6.44 ± 0.16 and 9.27 ± 0.04 MPa for the scaffolds containing 2.5 w/w% HAR and HAP, respectively. After immersing the scaffolds into simulated body fluid (SBF), the Ca concentration decreased by 55% for HAR- and 73% for HAP-containing scaffolds, showing the bioactivity of nHA-containing scaffolds. The results of cell attachment, proliferation, and viability of MG-63 cells cultured on the nanocomposites showed the positive effects of nHA. The results indicate that the nanocomposite scaffolds, especially HAP-containing ones, can be suitable for bone tissue engineering applications.