Amur corktree (Phellodendron amurense), a rare tree species in China, is also a medicinal plant containing berberine, jatrorrhizine and palmatine as its main effective ingredients. In order to examine the impact of light intensity on the contents of the three main effective alkaloidals in this plant, we designed different light intensity (100%, 75%, 50% and 25% of full sunlight) to treat the seedlings and determined their contents of berberine, jatrorrhizine, and palmatine. The results showed that full-sunlight treatment was the highest in the three alkaloids content compared with the other weaker light-intensity treatments, while the 75% full-sunlight treatment was highest in biomass production. Therefore the 75% full-sunlight treatment is recommended in terms of the production of the three alkaloids, because it is the highest if we consider biomass and alkaloids contents simultaneously.