Purpose: This study evaluated the capability of bone formation with silk fibroin/nano-hydroxyapatite/corn starch composite scaffold as a bone defect replacement matrix when grafted in a calvarial bone defect of rabbits in vivo. Methods: Ten New Zealand white rabbits were used for this study and bilateral round-shaped defects were formed in the parietal bone (diameter: 8.0 mm). The silk fibroin 10% nano-hydroxyapatite/30% corn starch/60% composite scaffold was grafted into the right parietal bone (experimental group). The left side (control group) was grafted with a nano-hydroxyapatite (30%)/corn starch (70%) scaffold. The animals were sacrificed at 4 weeks and 8 weeks. A micro-computerized tomography (μCT) of each specimen was taken. Subsequently, the specimens were decalcified and stained with Masson`s trichrome for histological and histomorphometric analysis. Results: The average μCT and histomorphometric measures of bone formation were higher in the control group than in the experimental group at 4 weeks and 8 weeks after surgery though not statistically significant ( P＞0.05). Conclusion: The rabbit calvarial defect was not successfully repaired by silk fibroin/nano-hydroxyapatite/corn starch composite scaffold and may have been due to an inflammatory reaction caused by silk powder. In the future, the development of composite bone graft material based on various components should be performed with caution.