Color indirect effects (CIE) means the physiological and psychological effects of color resulting from color vision. In this paper, we study CIE from the viewpoints of the integrated western and Chinese traditional medicine and the time quantum theory established by C. Y. Liu et al., respectively, and then put forward the color-automatic-nervous-subsystem model that could color excites parasympathetic subsystem and hot color excites sympathetic subsystem. Our theory is in agreement with modern color vision theory, and moreover, it leads to the resolution of the conflict between the color code theory and the time code theory oncolor vision. For the latitude phenomena on athlete stars number and the average lifespan, we also discuss the possibility of UV vision. The applications of our theory lead to our succeeding in explaining a number of physiological and psychological effects of color, in explaining the effects of age on color vision, and in explaining the Chinese chromophototherapy. We also discuss its application to neuroimmunology. This research provides the foundation of the clinical applications of chromophototherapy.