In this study, diploid, triploid, and tetraploid Crassostrea gigas samples were subjected to gas chromatography and ion mobility (GC-IMS) to identify and analyze volatile compounds and flavor fingerprints under conditions of high-temperature incubation. The GC-IMS technology identified a total of 54 volatile components in C. gigas. The contents of 1-octen-3-ol, butyl pentanoate, p-methyl anisole, and 2-methyl-2-hepten-6-one in male oysters were significantly higher than in females, while the contents of phenylacetaldehyde, benzaldehyde, 2-ethyl-3-methylpyrazine, 2-ethylfuran, and 2,4-hexadienal in female oysters were significantly higher than in males. The contents of non-3-en-2-one-M and 1-pentanol in diploids were significantly higher than in triploids and tetraploids, while the content of 2,4-hexadienal in tetraploids was significantly higher than in diploids and tetraploids. The contents of ethyl acetate, ethyl-2-butenoate, and butanal in tetraploids were significantly higher than those in diploids and triploids. The results of a principal components analysis showed that different samples were relatively independently clustered, allowing the ability to distinguish different oyster samples. The chemical fingerprints of volatile compounds of C. gigas with different ploidy and gender under high-temperature incubation were established, and the volatile substance contours of C. gigas were visualized. The results provide a reference for distinguishing the ploidy and gender of C. gigas under conditions of high-temperature incubation.