Hydroxyapatite (HAP) is promising for the clinical treatment of bone defects because of its excellent biocompatibility and osteo-conductivity. However, highly porous HAP scaffolds usually exhibit high brittleness and poor mechanical properties, thus organic constituents are usually added to form composite materials. In this work, a highly porous and elastic aerogel made from ultralong HAP nanowires with ultrahigh porosity (∼98.5%), excellent elasticity and suitable porous structure is prepared as the high-performance scaffold for bone defect repair. The highly porous structure of the as-prepared aerogel is beneficial to bone ingrowth and matter/fluid transfer, and the high elasticity can ensure the structural integrity of the scaffold during bone regeneration. Therefore, the HAP nanowire aerogel scaffold can promote the adhesion, proliferation and migration of rat bone marrow derived mesenchymal stem cells (rBMSCs), and elevate the protein expression of osteogenesis and angiogenesis related genes. The in vivo experimental results demonstrate that the HAP nanowire aerogel scaffold is favorable for the ingrowth of new bone and blood vessels, and thus can greatly accelerate bone regeneration and neovascularization. The as-prepared HAP nanowire aerogel scaffold shows promising potential for biomedical applications such as bone defect repair.