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The establishment and application of a two-crop-a-year cultivation system depends on the particularity of climatic conditions in subtropical regions. The different temperature, light, and water conditions throughout the growing season of summer and winter grapes are the fundamental reasons for differences in primary and secondary metabolites. We performed ultra-high-performance liquid chromatography–triple quadrupole mass spectrometry (UPLC-QQQ-MS)-based metabolomics on ‘Kyoho’ grapes under a two-crop-a-year cultivation system. In total, 1062 metabolites were identified and classified into 10 different categories, while flavonoids were the largest group, with 285 metabolites. Moreover, 876 metabolites were different among the four developmental stages, and 551 were different between the summer and winter grapes during the same growth period. Hierarchical clustering analysis (HCA) and principal component analysis (PCA) clearly distinguished developmental and growth-season differences based on the detected metabolites. Of note, flavonoids were the most important compounds responsible for the differences in berry composition during the growth and developmental seasons. The content of most flavonoids was higher in the winter grapes, but some were also found at higher levels in summer grapes, such as kaempferol-4′-O-glucoside, leucocyanidin, and cyanidin-3-O-glucosylglucoside. Additionally, myricetin-3-O-arabinoside was consistently higher in winter grapes than in summer grapes during all four developmental stages. The extreme high temperature and higher relative humidity were important reasons for the lower flavonoid content in the summer grapes than in the winter grapes. Moreover, the stronger light intensity in the early development of the winter grapes had a positive effect on the accumulation of flavonoids, especially flavonols and flavan-3-ols. This study provides new insights into the metabolism of flavonoids in grapes under a two-crop-a-year cultivation system and explores the climatic causes of the differences in the metabolites in the two crops of grapes.