Herein, we report microwave-assisted hydrothermal rapid synthesis of amorphous calcium phosphate (ACP) nanoparticles and hydroxyapatite (HAP) microspheres using biocompatible biomolecule cytidine 5′-triphosphate disodium salt (CTP) as an organic phosphorus source. In this method, CTP molecules are hydrolyzed to produce phosphate ions under microwave hydrothermal conditions, and these phosphate ions react with pre-existing calcium ions to form CaP products. The effects of experimental conditions on the morphology and crystal phase of the products are investigated. Cytidine triphosphate is a kind of pyrimidine nucleoside triphosphate which is also a key substrate in the synthesis of RNA. CTP is a high-energy molecule similar to ATP; it is a coenzyme in metabolic reactions like the synthesis of glycerophospholipids and glycosylation of proteins. The chemical structure of CTP is shown below. It consists of cytidine and three phosphate groups and can be a potential phosphate source for the synthesis of CaP materials.