The invention relates to gromwell pigment micro-capsules and a preparation method thereof. The preparation method comprises the following steps: totally dissolving 1 part by weight of ethyl cellulose into 4 to 30 parts by volume of dichloromethane; then adding extract of gromwell pigment and shaking to dissolve the extract of gromwell pigment; standing for 30 min; adding the obtained solution into 0.01 to 0.04 percent by mass of aqueous solution of sodium dodecyl sulfate with stirring; stirring for 2 h at a temperature of 10 to 30 DEG C; decompressing and carrying out pumping filtration; washing the obtained solid for three times by water; and after pumping, placing the obtained product into a drying box to dry so as to obtain the micro-capsules. According to the invention, the gromwell pigment micro-capsules and the preparation method thereof have the advantages that by carrying out microencapsulation after refining a medicament, the stability of the medicament is improved, the objectionable odor is reduced, the inactivation of the medicament in the gastrointestinal tract is prevented, the irritation of the medicament to the gastrointestinal tract is reduced, the release of the medicament is slowed down or controlled, the compatibility variation of the medicament is avoided, the medicament concentration is centralized to a target region, the biological activity of the medicament is stabilized, the gromwell pigment micro-capsules are beneficial for taking the curative effect and the like.