Phellodendron amurense Rupr. (Rutaceae) is a deciduous tree commonly called the Amur cork tree. The bark of P. amurense has been widely used in China, Japan, and Korea for hundreds of years for its anti-inflammatory and anti-tumor activities. It is regarded as a rich source of pharmaceutically important isoquinoline alkaloids, including berberine and jatrorrhizine. Berberine currently is recommended in China for the treatment of gastroenteritis, dysentery, tuberculosis, scarlet fever, acute tonsillitis, and respiratory tract infections. The substantial increase in its exploitation has caused serious damage to wild populations. At present, large areas of wild P. amurense trees are rare, and the species is severely endangered in China. Its extensive medicinal use has raised interest in its cultivation. The quantities of secondary metabolites in plants, including the P. amurense species, vary across habitats, geographical locations, seasons, and parts of the plant. The generation and variation of secondary metabolites has a stronger correlation and dependence on the environment than primary metabolites. The synthesis and accumulation of secondary metabolites are not only significantly affected by genetics, but also by environmental factors such as light, temperature, and moisture. Therefore, secondary metabolite levels within a species may differ among geographic populations. However, few studies have assessed variation in alkaloid content in P. amurense. This study attempted to explore alkaloid content variance of P. amurense among various habitats in Northeastern China. The berberine and jatrorrhizine contents in different parts (root bark, trunk bark, perennial branch bark, annual branch and leaf) were measured; and the seasonal and geographical variances of the two kinds of alkaloids in organs were analysed by high performance liquid chromatography(HPLC). The results showed that the seasonal content sequence of berberine and jatrorrhizine in different parts were the same root bark > trunk bark > perennial branch bark > annual branch > leaf. The contents of berberine in various parts increased from spring to summer but fell in aunumn. The contents of jatrorrhizine in different parts did not directly line up with the seasonal variation:jatrorrhizine in root bark and trunk bark gradually increased with the season passing, but the enhanced value was not obvious in summer; by autumn however, it accumulated massively. For the perennial branch barks, annual branches and leaves, the jatrorrhizine dropped from spring to summer, and increased in autumn. Along the latitude scale, the two kinds of alkaloids had the significant geographical variance. Normally, the content of alkaloids decreased gradually with the latitude enhancing, and reached the lowest value at N44°, and then reversed slightly. In the northeast China, the low latitude areas (such as Fengcheng and surrounding areas) could be confirmed for breeding and qualified medicine provenance of P. amurense, the raw material collection should be progressed in the summer or autumn better, and consider replaced trunk bark with perennial branch bark. The above results would help us to know the distribution regulation of the two kinds of alkaloids on multiple scales and provide the theoretical support for optimal cultivation and efficient, sustainable utilization of the natural resources found in P. amurense.