Abstract: Phellodendron amurense Rupr. is an endangered species and common medicinal plant with a long history in China. However, wild resources suffered severe damage from the 1960s to 1990s, and have, thus far, exhibited poor recovery. In this study, we researched population density and structure based on an extensive survey of 38 wild populations in the Yanshan, Qianshan, Changbaishan, Zhangguangcailing and Xiaoxing'anling mountains in norther and northeastern China, and applied HPLC to research the regional characteristics of alkaloid composition, including that of berberine, palmatine, phellodendrine, magnoflorine, and jatrorrhizine. The population structure of P. amurense showed a spindle shape, with the percentage of young and adult individuals being 13.9% and 68.0%, respectively. Overall, this showed a severe recession trend and seriously threatened condition due to the low numbers of young plants and insufficient natural regeneration. Chemical data showed that berberine, palmatine, phellodendrine, and total alkaloid content in P. amurense was the highest in Qianshan Mountain and the lowest in Xiaoxing'anling Mountain, with both showing significant differences compared with contents from the other three mountains. We conclud that the wild population distribution area of P. amurense is declining in China. Furthermore, the population age structure shows a decreasing trend and populations with few individuals have not managed self-restoration. The alkaloid content of P. amurense from low latitude areas, such as Qianshan Mountain, is significantly higher, which should be taken into consideration in regards to medicinal production.