Abstract: branch,leaf and root in mature age phase had the significant seasonal variance, the content of most organs (except leaf) got the maximum value in summer, the jatrorrhizine content of leaf reached the maximum in spring in all 3 age phases, and the organ content sequence of jatrorrhizine was root (0.84 mg/ g), trunk, perennial branch, annual branch and leaf.Secondary metabolites of berberine, palmatine and jatrorrhizine are important medicinal alkaloids from amur cork tree(Phellodendron amurense), we sampled 65 natural trees of different ages in 5 forestry bureaus of Jilin Province, northeastern China. The variations of three alkaloid contents in organs were analyzed among different seasons with RP-HPLC. The results were shown as follows: the berberine contents of root, perennial branch, annual branch and leaf existed significant variance with the season changing, and the content values of root, perennial branch and annual branch reached minimum in summer basically, the berberine content of leaf increased from spring to autumn at all 3 age phases, and the variance ranged between 0.017 and 0.124 mg/ g, the berberine content sequence of organs was root (24.27 mg/ g in average), trunk, perennial branch, annual branch and leaf; the palmatine content of root, trunk, annual branch, leaf and the perennial branch in juvenile phase got the significant seasonal variance, the content of root, trunk, annual branch and the perennial branch in juvenile phase reached the maximum value in autumn coincidently, the palmatine content of leaves got the maximum value in all 3 age phases in spring, and the organ content sequence of palmatine was trunk (7.02 mg/ g in average ), perennial branch, root, annual branch; the jatrorrhizine content of trunk, perennial branch, annual