The invention discloses a pure traditional Chinese medicine prescription for treating toothache and a preparation method thereof. The pure traditional Chinese medicine prescription is prepared from the following components in parts by weight: 30-35 parts of fresh aconitum gymnandrum rhizome, 20-23 parts of fresh aloe, 30-35 parts of fresh stevia rebaudiana, 10-12 parts of menthol, 13-15 parts of astragalus roots, 10-12 parts of asarum herbs, 10-12 parts of white peony roots, 15-18 parts of subprostrate sophora, 15-18 parts of prunella vulgaris, 10-18 parts of cloves, 5-6 parts of gutta-percha, 10-12 parts of sanguisorba officinalis and 13-15 parts of folium artemisiae argyi. According to the pure traditional Chinese medicine prescription for treating toothache, the astragalus roots have the characteristics of enhancing the immune function of the body, protecting the liver, promoting urination, resisting aging and stress, lowering blood pressure, realizing broad spectrum, resisting bacteria and the like; and the astragalus roots are matched with the prunella vulgaris, menthol and folium artemisiae argyi to achieve the effects of clearing away heat, diminishing inflammation, alleviating pain, refreshing mind and resisting bacteria.