The invention relates to an effective component of madder root, a preparation method and the application thereof; the preparation process of the effective component of madder root in the invention includes the following steps: step 1, the mixture of ethyl acetate and ethanol is used as solvent for extracting madder root; step 2, herb residue is extracted by ethanol to obtain extract; step 3, the extract is processed with chromatographic column chromatography to obtain eluate; step4, the eluate obtained by elution in the preparation of liquid phase chromatographic gradient is adopted; the mobile phase is water and acetonitrile, and the eluate of 48.0-52.0 min is collected to obtain the effective component.