The invention discloses an organic-inorganic hybrid nano pigment from natural plants and a preparation method and application thereof. The organic-inorganic hybrid nano pigment is a hybrid of naturalplant pigment, nano inorganic particles, a stabilizer and a surface modifier, wherein the weight ratio of natural plant pigment to nano inorganic particles to the stabilizer to the surface modifier is1: 0.2-3:0.2-0.7:0.2-1.5. The organic-inorganic hybrid nano pigment can be used in cosmetics, food, medicine, children's pigment and the like, and has rich material source, high safety and health, complete color system, natural color tone, certain health care function and relatively bright color, has good dispersibility, photothermal stability and coloring power, which is especially suitable forcoloring tablet sugar coating, candy and high-end cosmetics, and also suitable for coloring daily chemical products, hair dyes, printing ink, rubber, children toys and underwear products, and has wideprospect.