In this study, GC-IMS was used to analyze the volatile component and flavor profiles ofCrassostrea gigasindividuals of different ploidy and gender. Principal component analysis was used to explore overall differences in flavor profiles, and a total of 54 volatile compounds were identified. The total volatile flavor contents in the edible parts of tetraploid oysters were significantly higher than in diploid and triploid oysters. The concentrations of ethyl (E)-2-butenoate and 1-penten-3-ol were significantly higher in triploid oysters than in diploid and tetraploid oysters. In addition, the volatile compounds propanoic acid, ethyl propanoate, 1-butanol, butanal, and 2-ethyl furan were significantly higher in females than in males. The volatile compounds p-methyl anisole, 3-octanone, 3-octanone, and (E)-2-heptenal were present in higher levels in male than in female oysters. Overall, different ploidy and gender of oysters are connected with different sensory characteristics, providing new insights for understanding the flavor characteristics of oysters.