The invention discloses a highland barley red yeast pigment and a preparation method thereof and application of the highland barley red yeast pigment in food, belongs to the technical field of biochemical products, and in particular relates to a red yeast pigment, an extraction method for the red yeast pigment and application of the red yeast pigment. The highland barley red yeast pigment is prepared by the following steps of: crushing highland barley red yeast, extracting with ethanol, concentrating and drying. The highland barley red yeast pigment has the advantages that the highland barley red yeast pigment extracted by using the method mainly contains six pigments, namely rubropunctatin, monascorabrin, monascin, ankaflavin, rubropunctamine and fmoc-allo-thr-oh by detection and analysis, the color value of the highland barley red yeast pigment reaches over 6000U/g and is improved by over 6 times compared with the color value (800u/g) of the highland barley red yeast raw material, and the highland barley red yeast pigment has good coloring capability. The highland barley red yeast pigment also contains multiple substances with health-care effect such as Monacolin K, gamma-aminobutyric acid, beta-glucan, fatty acid and ergosterol, so not only the highland barley red yeast pigment has the coloring effect, but also the health-care effect of the highland barley red yeast pigment is increased.