This study radiologically and histologically compared two bioresorbable bone substitutes with different compositions carbonate apatite (Cytrans ® Granules; CGs) and β-tricalcium phosphate (β-TCP) for vertical bone augmentation on a rat skull using a polytetrafluoroethylene (PTFE) tubes. This PTFE tube was placed at the center of the skull, fixed with Super Bond, and augmented with CGs or β-TCP granules. Specimens with surrounding tissue were harvested at 4, 8, and 12 weeks postoperatively, and radiological and histological evaluations were performed. The bone volume to total volume ratio (BV/TV) of the β-TCP-implanted group was markedly higher than that of the CG-implanted group at 4 and 12 weeks postoperatively. Compared to CGs, β-TCP exhibited the ability to form blood vessels into the graft material for a short period after transplantation, as well as an elevated production of collagen into β-TCP granules during the bone formation process.