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Biomaterial based scaffolds for treating large bone defects require excellent biocompatibility and osteoconductivity. Here we report on the fabrication of hydroxyapatite-dendritic mesoporous silica nanoparticles (HA-DMSN) based scaffolds with hierarchical micro-pores (5 µm) and nano-pores (6.4 nm), and their application for bone regeneration. The in vitro studies demonstrated good biocompatibility of dissolution extracts, as well as enhanced osteogenic potential indicated by dose-dependent upregulation of bone marker gene expression (osteocalcin gene (OCN), osteopontin gene (OPN), collagen type I alpha 1 gene (CoL1A1), runt-related transcription factor 2 gene (RUNX2), and integrin-binding sialoprotein gene (IBSP)), alkaline phosphatise (ALP) activity, and alizarin red staining. The in vivo studies showed that HA-DMSN scaffolds significantly increased bone formation in a rat cranial bone defect model after 4 weeks healing. Our study provides a simple method to fabricate promising inorganic scaffolds with hierarchical pores for bone tissue engineering.