The large yellow croaker is one of the most economically important fish in Zhoushan, Zhejiang Province, and is well known for its high protein and fat contents, fresh and tender meat, and soft taste. However, the mechanisms involved in its flavor changes during storage have yet to be revealed, although lipid oxidation has been considered to be one important process in determining such changes. Thus, to explore the changes in the flavor of large yellow croaker fish meat during different storage periods, the main physical and chemical characteristics of the fish meat, including the acid value, peroxide value, p-anisidine value, conjugated diene value, and identities of the various flavor substances, were investigated and analyzed by multivariable methods, including headspace gas chromatography–ion mobility spectrometry (GC-IMS) and principal component analysis (PCA). It was found that after 60 d storage, the types and contents of the aldehyde and ketone aroma components increased significantly, while after 120 d, the contents of ketones (2-butanone), alcohols (1-propanethiol), and aldehydes (n-nonanal) decreased significantly. More specifically, aldehyde components dominated over ketones and lipids, while the n-nonanal content showed a downward trend during storage, and the 3-methylbutanol (trimer), 3-methylbutanol (dimer, D), 3-pentanone (D), and 3-pentanone (monomer) contents increased, whereas these compounds were identified as the key components affecting the fish meat flavor. Furthermore, after 120 d storage, the number of different flavor components reached its highest value, thereby confirming that the storage time influences the flavor of large yellow croaker fish. In this context, it should be noted that many of these compounds form through the Maillard reaction to accelerate the deterioration of fish meat. It was also found that after storage for 120 d, the physical indices of large yellow croaker meat showed significant changes, and its physicochemical properties varied. These results therefore demonstrate that a combination of GC-IMS and PCA can be used to identify the differences in flavor components present in fish meat during storage. Our study provides useful knowledge for understanding the different flavors associated with fish meat products during and following storage.