Sophora tonkinensis is widely used as traditional Chinese medicine for treating the swelling of the gums and tongue and mouth sores due to flame stomach fire. It is mainly origin from Guangxi, Sichuan provinces of China. Alkaloids are considered as the major bioactive components. A method was established for identifying alkaloids in S. tonkinensis root by UPLC-Q-TOF-MS/MS and was applied in characterizing alkaloids in S. tonkinensis root of two different habitats. Consequently, twenty-four alkaloids including six new compounds were identified in S. tonkinensis root. Additionally, the difference of alkaloids in S. tonkinensis from Guozhou, Sichuan province was investigated. In the present study, we firstly characterize total alkaloids in S. tonkinensis root by UPLC-Q-TOF-MS/MS and firstly established the characteristic fragmentation pathway of alkaloids with hydroxy in S. tonkinensis root.