In this study, four kinds of Longjing tea, the famous flat green tea and the protected geographical indication product in China, were used to explore the quality difference of the same green tea due to the cultivar, geographic origin, and storage time under the premise of consistent picking conditions and processing technology using the widely targeted metabolomics. Results showed that 483 flavonoid metabolites with 10 subgroups of flavonoids were screened and 118 differential flavonoid metabolites were identified. The number and subgroups of differential flavonoid metabolites produced by different cultivars of Longjing tea were the largest, followed by storage time, and third by the geographic origin. Glycosidification and methylation or methoxylation were the main structural modifications of differential flavonoid metabolites. This study has enriched the understanding of the effects of the cultivar, the geographic origin, and the storage time on the flavonoid metabolic profiles of Longjing tea, and provided worthy information for the traceability of green tea.