Three types of calcium-deficient apatite fibers (Ca-def AF) were synthesized by a homogeneous precipitation method using starting solution with Ca/P ratios of 1.00, 1.50 and 1.67, and then the resulting fibers were characterized by XRD, FT-IR and SEM. Especially, the microstructure including strain and defect of individual Ca-def AF was examined by transmission electron microscopy (TEM). All the resulting Ca-def AFs had a single phase of apatite, and contained carbonate ions. These fibers were of single crystal, and highly strained. However, when Ca-def AFs were heated to higher than 800 °C, they changed to HAp and TCP biphases. The content of the carbonate group in the Ca-def AFs decreased with heating temperature.