The invention discloses a method to extract, separate and purify natural pigment especially high purity lutein, which comprises the following steps: extracting patuletin; getting concrete; using as raw material; dissolving in mixed solvent of alcohol and tetrahydrofuran; adding into KOH water solution; heating the mixed liquid; saponifying; adding into deionized water; crystallizing; filtering; drying; getting lutein rough product; extracting with acetone; evaporating the acetone; leaching with alcohol; getting purified free state lutein. This invention possesses high purity, which is fit forraw material of food additive and medical health products.