Thermophilic bacterial strains HEN-Qn1 were incubated at 60 °C in a solution containing calcium chloride. With slow release of CO2 metabolic end products from the bacteria, CaCO3 nanomaterials were found after 12 h through a transmission electron microscope (TEM). CaCO3 nanorods were obtained extracellularly, whereas a unique morphology of nanosphere was observed intracelluarly. A single crystal was further characterized by electron pattern (ED) and X-ray powder diffraction (XRD). Moreover, a putative mechanism has been proposed based on theoretical analyses and experimental evidences. These results indicated that thermophilic bacteria had a well-controlled effect during the crystal growth of inorganic materials, which provided us a promising application of bacteria in biosynthesis of nanomaterials.