Light is the primary stimulus for regulating circadian rhythms, seasonal cycles, and neuroendocrine responses in many species, including humans. The major circadian pacemaker in the hypothalamic suprachiasmatic nucleus is entrained to the light/dark cycles from the outside world by circadian photoreceptors which are functionally characterized by the direct sensitivity to light with broad spectrum and the relatively high stability. Chromophototherapy mediated by the color indirect effect (CIE), the physiological and psychological effects of color resulting from color vision, is functionally characterized by the sensitivity to light with narrow spectrum and the relatively low stability. In this paper, the mechanism of chromophototherapy used in sports medicine and rehabilitation, especially in treating overtraining syndrome (OTS), was discussed. Although several hypotheses and the corresponding OTS treatments have been proposed, each only explains and treats a selective aspect of OTS. On the one hand, an autonomic or neuroendocrine imbalance is hypothesized as underlying by Lehmann et al so that the described functional alterations of pituitary-adrenal axis and sympathetic system can explain persistent performance incompetence in affected athletes beside additional mechanisms. On the other hand, cold color (green, blue or violet) excites parasympathetic subsystem and hot color (red, orange or yellow) excites sympathetic subsystem for chromophototherapy. The conclusion was then drown that chromophototherapy might be a good therapy to treat OTS.