The invention discloses an extract composite preparation for treating oral ulcer and a preparation method thereof. The extract composite preparation is prepared by mixing inula cappa, glycyrrhiza, pearl and borneol. In the invention, the inula cappa and the glycyrrhiza are respectively extracted, purified and refined to obtain inula cappa total flavonoid extract, glycyrrhiza total flavonoids and total saponin extract, and the composite preparation of the extracts is prepared fromthe inula cappa total flavonoid extract, the glycyrrhiza total flavonoids and the total saponin extract as well as pearl fine powder and borneol fine powder after crushing. Compared with the prior art, the invention respectively carries out purification, separation and concentration on extract solution, has enriched effective components, better keeps the characteristics of a Chinese herbal medicine compound preparation, efficiently lowers the side effects of medicines and enhances the curative effect, thereby enhancing and ensuring the quality of a product.