The invention relates to a pigment paper chromatography separation method, in particular to a chloroplast pigment paper chromatography separation method. The method includes the steps that first, pigment extract is prepared and stored in a place kept out of sun for use; then, cylindrical filter paper is made; finally, sample application is performed, after sample application pigment is dried through an electric hair drier, a small hole is made in the center of the sample application pigment, one end of the cylindrical filter paper is inserted in the small hole, the other end, namely a base end, of the cylindrical filter paper is placed in a culture dish with layer unfolding agent, the round filter paper subjected to the sample application is placed on the culture dish, and chromatography starts. After four colored ribbons (beta-carotene, lutein, chlorophyll a and chlorophyll b) are all separated, the chromatography is completed. According to the method, while the chromatography separation effect, for instance, the color of the colored ribbons is pure and the edges of the colored ribbons are clear, is improved, investment of a chromatography container is reduced and saved by 60 percent, tedious processing of the chromatography filter paper is reduced, and toxic pollution generated when acetone serves as the extraction agent, and the carbon tetrachloride serves as the layer unfolding agent is reduced. The separation method is good in separation effect, time and labor are saved, and environmental pollution and toxicity are reduced.