Calcium phosphates (CPs), as the major inorganic component of biological hard tissues, have been investigated for applications as biomaterials owing to their excellent biocompatibility. However, the traditional synthetic CPs are usually prepared from inorganic phosphorus and calcium sources. Herein, we report a new strategy for the synthesis of a variety of calcium–phosphate nanostructures, including porous amorphous calcium phosphate (ACP) microspheres, hydroxyapatite (HAP) nanorods, and ACP/HAP composite microspheres, by using fructose 1,6-bisphosphate trisodium salt (FBP) as an organic phosphorus source in aqueous solution in a rapid microwave-assisted hydrothermal reaction. The important role of FBP and the effect of the experimental conditions on the formation and evolution of the CPs nanostructures were investigated. The crystal phase and composition of the as-prepared products were characterized by powder X-ray diffraction (XRD), FTIR spectroscopy, and thermogravimetric (TGA) analysis and the morphologies of the products were characterized by SEM and TEM. This method is facile, rapid, surfactant-free, and environmentally friendly. The as-prepared porous ACP microspheres have a relatively high drug-loading capacity and good sustained drug-release behavior; thus, they are promising for applications in drug delivery.