The invention relates to a yin-yang moxibustion prescription and a preparation method thereof. The yin-yang moxibustion prescription comprises a yang prescription and a yin prescription. The yang prescription comprises ginseng, radix astragali, rhizoma zingiberis, radix angelicae sinensis, pseudo-ginseng, radix glycyrrhizae, rhizoma ligusticum wallichii, radix polygonum multiflorum, cortex eucommiae, herba menthae, earthworms, poria cocos, rhizoma acori calami, fructus schisandrae chinensis and radix rehmanniae preparata. The yin prescription comprises ginseng, fructus schisandrae chinensis, radix ophiopogonis, rhizoma zingiberis, radix glycyrrhizae, radix angelicae sinensis, radix polygonum multiflorum, poria cocos, pseudo-ginseng, rhizoma gastrodiae, radix salviae miltiorrhizae, fructusfoeniculi, fructus aurantii, radix codonopsis and herba menthae. According to the yin-yang moxibustion prescription, different kinds of natural Chinese medicine are selected and proportioned accordingto weight to prepare the yin-yang moxibustion prescription with the efficacy of promoting yang to induce resuscitation, nourishing yin and blood, harmonizing the five internal organs, tonifying the kidney, increasing essence, inducing resuscitation, refreshing the brain and harmonizing the five internal organs. The yin-yang moxibustion prescription is scientific in compatibility, high in permeability, obvious in curative effect and short in effect buffer time, and has an effective rate higher than 95% in treatment of the symptoms such as pain of the shoulders and neck, soreness of the lumbarvertebra, lumbar muscle strain, sciatica, fatigue and weakness of the whole body and insomnia. Moreover, the preparation method is simple and convenient to use.