Background: The seeds of Polygonatum cyrtonema Hua have dormancy phenomenon. Previous studies have shown that sand storage factors effects of the seed dormancy of P. cyrtonema Hua seeds and enhance the seed germination process. Subsequently, metabolic activities and different changes during the sand storage and germination process of P. cyrtonema Hua seed has not been heavily researched.Results: In this study the changes in the metabolites of P. cyrtonema Hua seeds at different sand storage times and germination stages, we used untargeted metabolomics to determine them. Most of the sugar and glycoside contents in seed coat increased after 30 d on the other hand, in peeled seeds increased at 30 d and decreased at 60 d after sand storage treatment. The content of proline and benzoic acid decreased in the seed coat after sand storage. PCA, OPLS-DA and HCA showed that the contents of most metabolites increased after 7 d and decreased after 14 d of seed germination. The process of 7 d to 14 d was the key stage of seed germination of P. cyrtonema Hua. Differential metabolic pathway analysis showed that seed germination was controlled by multiple metabolic pathways. Metabolic correlation revealed the interdependence between seed germination metabolites and metabolic pathways. Conclusion: Sand storage can significantly increase the rate of seed germination and play a vital role in seed dormancy of P. cyrtonema Hua. There was inherent differences in metabolites during different storage time and germination stages in P. cyrtonema Hua. Our work provides a first glimpse of the metabolome in seed germination of P. cyrtonema Hua, and provides a valuable informations for revealing the mechanism of breaking seed dormancy.