The essence-qi-spirit theory is an important part of traditional Chinese medicine， whose steady state is the material and functional basis for the balance of yin and yang in the body， making the essence， qi and spirit integrated， and body and spirit harmonized. Based on this theory， it is proposed that essence and qi depletion， spirit dissipation and qi dispersion， disharmony between yin and yang is the main pathogenesis of sleep disorders. Therefore， the method of regulating and harmonzing yin and yang by essence gathering， qi nourishing and spirit storing can be used to treat sleep disorder. The biological clock system of the circadian rhythm of sleep is regulated by the molecular oscillation that is generated by the transcription of the biological clock gene， and is a clock gradually formed by orga-nisms constantly adapting to the laws of nature. As the material basis， power， and embodiment of sound and peaceful sleep， essence， qi and spirit can perceive and transmit natural signals， whose functions are similar to what is recognized by modern science that oscillation amplifies the rhythm signal， and synchronously regulates the expression signal of the biological clock gene， thereby forming a biological clock system with “input-oscillation-output” as the feedback cycle. It is believed that the regulation method of yin and yang by essence gathering， qi nourishing and spirit storing may comprehensively regulate the physiological activities through brain/ muscle aryl hydrocarbon receptor nuclear translocator-like protein 1 （BMAL1）/circadian locomotor output cycles kaput （CLOCK）-period protein （PER）/ cryptochrome （CRY） transcriptional feedback loop， thereby adapting to the natural environment changes， playing an active role in the treatment of sleep disorders， and provideing a new idea for traditional Chinese medicine to reshape the molecular regulation system of the endogenous biological clock to prevent and treat sleep disorders.