Hair follicles enjoy continual cycle of anagen, catagen and telogen all life. They not only provide a unique opportunity to study the physiological mechanism of organ regeneration, but also benefit to guide the treatment of organ repair in regenerative medicine. Usually, the histological examination as a gold standard has been applied to determine the stage of hair follicle cycle, but noninvasive classification of hair cycle in vivo remains unsolved. In this study, the thermal infrared imager was applied to measure the temperature change of mouse dorsal skin with hair follicle cycle, and the change of diffuse reflectance was monitored by the optical fiber spectrometer. Histological examination was used to verify the hair follicle stages. The results indicated that the skin temperature increased at the beginning of anagen. After having stayed a high value for several days, the temperature began to decrease. At the same time, the skin diffuse reflectance decreased until the end of this period. Then the temperature increased gradually after slightly decreased when the hair follicle entered into catagen stage, and the diffuse reflectance increased at this time. In telogen, both the temperature and the diffuse reflectance went back to a steady state all the time. Sub-stages of hair follicle cycle could be distinguished based on the joint curves. This study provided a new method to noninvasively recognize the hair follicle stage, and should be valuable for the basic and therapeutic investigations on hair regeneration.