Platycodon grandiflorus (Jacq.) A. DC. is widely cultivated across the south and north of China. Its root, Platycodonis radix, is commonly used as a vegetable, functional food, and traditional herbal medicine with various biological benefits. It is critical to fully clarify the chemical composition of Platycodonis radix for the sake of the food industry and traditional herb markets. In this study, a strategy of metabolome and lipidome profiling based on ultra-high performance liquid chromatography coupled to ion mobility-quadrupole time of flight mass spectrometry (UPLC-IM-QTOF-MS) was developed to reveal the overall chemical composition of Platycodonis radix. IN particular, comprehensive lipidome profiling was first performed for Platycodonis radix, in which 170 lipid molecular species including 55.9% glycerophospholipids, 31.2% glycerolipids, and 12.9% sphingolipids were identified. Platycodonis radix from two major production regions in China, Inner Mongolia and Anhui province, were collected and analyzed by the MS based approach combined with multivariate statistical analysis from both the metabolome and lipidome aspects. This study threw focus on the profiling investigations of Platycodonis radix from different growing regions and provided new potential in the lipidome analysis of medicinal food.