Hydroxyapatite (HA) nanorods were synthesized by hydrothermal process using anhydrous CaCl2 and (NH4)2HPO4 as raw materials, urea was used as a homogeneous precipitation agent; hexadecyltrimethy ammonium bromide (CTAB) was used as a template agent. Phase composition and microstructure of the products were characterized via X-ray diffractometer (XRD), scanning electron microscope (SEM) and transmission electron microscopy (TEM). The results show that the morphologies of HA nanorods can be controllably fine-tuning by changing the reaction temperature and time. Hexagonal single crystal HA nanorods single structure can be obtained at 120℃ for hydrothermal 12 h, its length is about 0.5-1.0 μm, diameter is about 15-30 nm. Finally, the role of CTAB was studied by the formation process of nanorods crystalline structure in details, and verified by experiment.