BACKGROUND: In guided bone regeneration (GBR) technique, many materials have been used for improving biological effectiveness by adding on membranes. The new membrane which was constructed with chitin-fibroin-hydroxyapatite (CNF/HAP) was compared with a collagen membrane (Bio-Gide®) by means of micro-computed tomography. METHODS: Fifty-four rats were used in this study. A critical-sized (8 mm) bony defect was created in the calvaria with a trephine bur. The CNF/HAP membrane was prepared by thermally induced phase separation. In the experimental group (n = 18), the CNF/HAP membrane was used to cover the bony defect, and in the control group (n = 18), a resorbable collagen membrane (Bio-Gide®) was used. In the negative control group (n = 18), no membrane was used. In each group, six animals were euthanized at 2, 4, and 8 weeks after surgery. The specimens were analyzed using micro-CT. RESULTS: Bone volume (BV) and bone mineral density (BMD) of the new bone showed significant difference between the negative control group and membrane groups (P < 0.05). However, between two membranes, the difference was not significant. CONCLUSIONS: The CNF/HAP membrane has significant effect on the new bone formation and has the potential to be applied for guided bone regeneration.