Many efforts have been made in fabricating three-dimensional (3D) ordered hydroxyapatite (Ca10(PO4)6(OH)2, HAp) nanostructures due to their growing applications as a bone cement, drug deliverer, tooth paste additive, dental implant, gas sensor, ion exchange, catalyst, etc. Here, we developed a new synthetic route to 3D HAp-based hollow microspheres through a water-soluble biopolymer (polyaspartic acid) assisted assembly from HAp nanorods. The as-obtained products were characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), Fourier transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), high-resolution TEM (HRTEM), and Brunauer–Emmett–Teller (BET) gas sorptometry. SEM and TEM results showed that 3D HAp hollow microspheres are constructed by a number of one-dimensional (1D) nanorods as primary building units. The influences of the additive polyaspartic acid and reaction time on final morphology and assembled structure of the products were systematically investigated. On the basis of our experimental results, a phenomenological elucidation of the mechanism for growth of the hollow HAp architectures has been proposed. The time-dependent experiments unveil that the HAp hollow microspheres are fabricated following initial formation and subsequent transformation of amorphous calcium phosphate (ACP) spheres. In-depth investigations, based on control experiments and FT-IR, EDX, and XPS analyses, reveal that polyaspartic acid acts as both a chelating and a surface capping agent in the synthesis process. First, polyaspartic acid molecules via calcium ion accumulation induce formation of ACP. At the subsequent stage Ostwald ripening contributes to formation of the hollow microspheres, and polyaspartic acid molecules capping to the surface of HAp crystallites control growth of the short nanorod subunits. Moreover, the adsorption experiments of the hierarchical hollow HAp for different heavy metal ions were conducted, and the results exhibit that the hierarchical hollow HAp have unique selective adsorption activity for heavy metal Pb2+. In-depth investigation is still in progress.