The invention discloses a traditional Chinese medicine composition for treating periodontitis and a preparation method and application thereof. The traditional Chinese medicine is prepared from, by mass, 18-25 parts of Chinese yams, 11-14 parts of wild chrysanthemum flowers and 1-2 parts of herbs of peltateleaf meadowrue; the herbs of peltateleaf meadowrue are taken and calcined on fire, after cooling is conducted, the calcined herbs of peltateleaf meadowrue are put into a mortar for grinding and sieving, and fine powder is obtained; the Chinese yams and the wild chrysanthemum flowers are taken and cleaned, water is added for soaking, extracting by heating is conducted for two times, filtrate is combined, filtration is conducted, and the filtrate is concentrated to thick paste; the fine powder is mixed with the thick paste, and pills are prepared. The traditional Chinese medicine composition for treating the periodontitis has the effects of clearing heat, removing toxicity, decreasing swelling to relieving pain, activating the blood, dissipating blood stasis, settling pain and healing sores, and the curative effects on treating symptoms, caused by periodontitis, of tooth mobility, gingival atrophy, gingival swelling and bleeding, ozostomia, calculus and tartar accumulation and tooth ache caused by sour, sweet, cold and hot food are obvious. According to the traditional Chinese medicine composition for treating the periodontitis, the raw materials are easy to obtain, the cost is low, toxic and side effects do not exist, and the the traditional Chinese medicine composition has the advantages of being short in treatment cycle, obvious and reliable in curative effect and not prone to relapse after healing.