Phellodendron amurense is a rare species and medicinal plant in China. The present investigation determined the biomass and contents of berberine, jatrorrhizine, palmatine in the root and cortex of Amur corktree seedlings after one year′s shading with red, yellow, blue and green films. The results showed that all the four treatments remarkably decreased the biomass and/or the contents of the three alkaloids. Color-film shading is not recommended in practice in terms of the Amur corktree seedlings growth and alkaloids accumulation.