The invention provides a natural pigment composition. The natural pigment comprises an emulsifier and two or more than two pigments of gardenia yellow pigment, curcumin, carithamine, citroxanthin, xanthophyll, riboflavin, capsaicin, monascus red pigment, bixa orettana pigment and gardenia blue. Natural pigments can prepare natural pigment compositions in different color systems and different tones in arbitrary proportions, such as yellow, orange, red, green and purple. Meanwhile, the natural pigment composition contains the emulsifier, so that the composition can be more uniform and more stable. Therefore, in the natural pigment composition provided by the invention, combinations of different natural pigments can overcome the defect of single pigment, for example, the light resistance of natural yellow pigment combined by the riboflavin, the curcumin and the like with poor light resistance and the gardenia yellow pigment with more stable light resistance is better than that of the riboflavin or the curcumin, thus the dosage can be reduced, and the cost can be reduced.