Polygonatum odoratum is a homology of medicine and food. Primary and secondary metabolites are the important material basis for its edible and medicinal values. However, the synthesis of metabolites is closely related to the variety and region. In this study, P. odoratum samples were collected from Hunan, Guangdong, Zhejiang and Jilin. Meanwhile, different varieties in Hunan, such as Zhushiwei, Gaohe, Ciwei, Tianmawei and wild P. odoratum were also collected. The non-targeted metabolomics technology based on ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was employed to identify the metabolites of P. odoratum. A total of 1 011 metabolites were identified in 30 samples of P. odoratum, which were classified into 18 categories including amino acids and derivatives, organic acids, benzene and its substituted derivatives, and lipids, etc. A metabolite dataset of P. odoratum from different regions and varieties was established. This dataset can provide support for the comprehensive evaluation of the quality of P. odoratum and its rational utilization.