The invention provides a natural pigment composition. The composition comprises an emulsifier, and two or more than two pigments selected from gardenia yellow pigment, curcumine, carthamin yellow, orange yellow pigment, xanthophylls, riboflavin, capsanthin, monascus red pigment, anattotree orange pigment and gardenia blue pigment. All the above natural pigments can be blended according to an arbitrary ratio to obtain the natural pigment composition with different color systems and different tones, such as yellow, orange, red, green and purple. The natural pigment composition contains the emulsifier, so the composition is uniform and stable. The combination of different natural pigments in the natural pigment composition makes up the defect of single pigments, for example, the light resistance of the natural yellow pigment composition obtained by combining riboflavin and curcumine with poor light resistance with stable gardenia blue pigment is better than that of riboflavin or curcumine, so the use amount is reduced, and the cost is reduced.