Biomaterial scaffolds have been widely used in tissue engineering. A functionalized self-assembled peptide scaffold named RADA16-OPD was designed by linking the short functional motif of osteopontine (OPN)-derived functional fragments SVVYGLR (OPD) to the C-terminus of the self-assembled peptide RADA16. Atomic force microscopy (AFM) was used to analyze the self-assembling peptide’s structural composition. The live/dead staining results showed that RADA16-OPD is not toxic to rASC. After creating a rat skull defect model artificially, micro-CT results revealed that the defect area treated with RADA16-OPD hydrogel had higher bone volume/total volume (BV/TV), a higher trabecular number (TB.N.), and higher bone density (BMD) at different treatment time points. Histological evaluation found that there was more new bone and mature collagen production in the RADA16-OPD group. Meanwhile, the RADA16-OPD group had higher expression of alkaline phosphatase (ALP) and osteocalcin (OCN) than the other two groups. Additionally, immunofluorescence revealed that the RADA16-OPD group had higher levels of platelet/endothelial cell adhesion molecule 1 (CD31) expression than the other two groups. It demonstrated the potential for clinical use of the RADA16-OPD peptide scaffold by promoting bone regeneration and blood vessel development in vivo.