We report here a facile strategy to fabricate three-dimensional (3D) hydroxyapatite (HA) architectures with well-defined long continuous interconnected pores by using electrospinning and biomimetic mineralization. To this end, a polymeric nanofiber (NF) scaffold with well-defined architecture was fabricated by electrospinning, and bone morphogenetic protein 2 (BMP2) was then adsorbed onto the chemically modified NFs through bio-conjugation. The 3D nanoporous HA architecture was finally fabricated by biomimetic mineralization of the NF-BMP2 hybrid in simulated body fluids and subsequent dissolution of NFs in hexafluoroisopropanol. The formation of NF-BMP2 hybrid was identified by confocal laser scanning microscopy analysis. The crystal structure of HA crystals formed on NFs was examined by X-ray diffraction. The chemical composition and interconnected porous structure of the created 3D HA architectures were measured by X-ray photoelectron spectroscopy, focused ion beam scanning electron microscopy, and transmission electron microscopy, respectively. This bottom-up strategy based on electrospinning and biomimetic mineralization opens up a new way to prepare diverse porous HA-based hybrid materials and shows great potential in drug delivery, gene transfer and tissue engineering.