This study aimed to establish that copper-deposited Diatom-biosilica have the potential and possibility for clinical applications in repairing bone defects in a state of inflammation, such as periodontitis. Treatment of alveolar bone defects caused by periodontitis is a major challenge for clinicians. To achieve better repair results, the material should not only be bone conductive but also have the ability to stimulate osteogenesis and angiogenesis at the lesion site. Copper (II) and silicon (IV) ions could react to form basic copper silicate, which promoted both osteogenesis and angiogenesis. The mineralized diatom (Cu-DBs) loaded with copper (II) ions were synthesized by processing diatom shells using a hydrothermal method. Periodontal ligament stem cells (PDLSCs) are used to detect the osteogenic properties of Cu-DBs at the gene and protein levels. Using a rat cranial defect model and a fullthickness skin incision model to test the osteogenic properties of Cu-DBs in vivo.Compared with untreated diatoms (DBs), Cu-DBs extract significantly promoted the expression of osteogenesis-related factors like ALP, RUNX2, BSP, OCN, and OPN in PDLSCs. In vivo experiments further confirmed that Cu-DBs could effectively stimulate the osteogenesis of a rat skull defect and promote angiogenesis, significantly inhibit the inflammatory responses to bone damages, and reduce the infiltration of inflammatory immune cells to the lesion site. Due to the unique chemical characteristics of Si 4+ and Cu 2+ ions, the Cu-DBs composite biomaterial could enhance the osteogenic differentiation of PDLSCS in vitro, as well as stimulate the osteogenesis of the rat in vivo.