Lilium davidii var. unicolor is an important variety of lily with high economic, ornamental and medicinal values. It is one of the best lilies which are edible in China. Here, we study the physiological changes of L. davidii var. unicolor at different growth stage (vegetative stage, early bloom stage, full bloom stage, late bloom stage, early dry stage and dormancy stage) and metabolomics analysis of mother bulb at three different stages (full bloom stage, late bloom stage and early dry stage). The fast changes in plant height and number of daughter bulbs occurred from vegetative stage to full bloom stage and then became slow in the followed stages. The fresh weight of daughter bulb increased significantly from vegetative stage to dormancy stage, and fresh weight of mother bulb increased obviously from vegetative stage to full bloom stage. Plant fresh weight increased first and then decreased. Non-targeted metabolomics were used to analyze the metabolism of mother bulbs at three stages. A total of 141 differential metabolites were identified. According to the metabolic pathways identified in KEGG database, we found that 15 differential metabolites were enriched in multiple metabolic pathways, including l-aspartic acid, l-valine, trehalose, arbutin, and salicylic acid. Furthermore, we found that the chlorophyll contents, maximal photochemical efficiency and actual photochemical efficiency all have the maximum value at full bloom stage and the carbohydrate content also changed significantly from full bloom stage to early dry stage, which were consistent with the results of metabolomics. Thus, we can conclude that full bloom stage to early dry stage is the key period and this period involves many differential metabolites, which play an important role in L. davidii var. unicolor growth.