In this work, the nonvolatile and volatile compounds were analyzed to investigate the effects of breeding and ploidy on the flavor of oysters. The oysters after breeding (November) exhibited enhanced flavor complexity characterized by malty and mushroom aromas, with diploid oysters displaying nutty aroma profiles, whereas triploid oysters demonstrated significantly higher intensity of fruity notes. Among oysters of different periods and ploidy, the November diploid oyster (ND) exhibited the most desirable flavor. This was primarily attributed to its significantly higher contents of adenosine 5'-monophosphate (AMP; 112.84 ± 1.56 mg/100 g), lactic acid (147.79 ± 8.98 mg/100 g), aspartic acid (45.28 ± 2.22 mg/100 g), and calcium ions (Ca2⁺; 1.45 ± 0.05 mg/g) compared to November triploid oyster (NT), March diploid oyster (MD), and March triploid oyster (MT). The equivalent umami concentration also showed a similar result (EUC: ND > NT > MD > MT), which was also confirmed by the results of the electronic tongue. The oysters included 14 aldehydes, 11 alcohols, 13 ketones, and 21 other compounds as analyzed by gas chromatography-ion mobility spectrometry. This study conducted the first comparative analysis of flavor profiles between diploid and triploid oysters through the lens of breeding, determined the optimal flavor period for each oyster, and provided scientific recommendations for the selection of raw materials for oyster products.