The invention provides agarwood extract with an enteritis inhibiting medicinal effect and a preparation method and application thereof. According to the agarwood extract with the enteritis inhibiting medicinal effect, agarwood produced through the whole body agarwood production technology is adopted as a raw material, and the agarwood extract is obtained through extraction and concentration. It is found through study that the agarwood extract has a remarkable colitis inhibiting function, can be used for preparing effective medicine and healthcare products for treating enteritis, is high in medicinal value and high in obtained economic benefit and has important significance on development of the whole agarwood industry.