Small yellow croaker, Larimichthys polyactis is one of the most important fishery resources in China. The phenotypes of different geographical groups are influenced by their migration patterns and may exhibit adaptive changes. To explore the morphological differentiation of small yellow croaker in different geographic populations, the reproductive and non-reproductive populations in the south Yellow Sea and the south-central East China Sea were used as the research objects. The analysis methods t-test, principal component analysis and the difference coefficient were used to systematically analyze 31 phenotypic traits of the small yellow croaker populations. The results indicated that the phenotypic traits of the south Yellow Sea population and the south- central East China Sea population vary widely. The average coefficients of variation during the reproductive period were 7.77% and 6.48%, respectively, and the coefficients of variation during the non-reproductive period were 8.65% and 7.62%, respectively. The variation intensity of the south Yellow Sea population was higher than that of the south-central East China Sea population, and the difference coefficient was primarily measured on the horizontal axis. Significant differences were detected between 15 traits in the reproductive periods and 16 traits in the non-reproductive periods (P＜0.05). There were significant differences among 7 traits in both periods, while the differences of these traits remained relatively stable within the population. The results of principal component analysis indicated that the cumulative contribution rate of the four principal component variances during the reproductive period was 48%, and the scores of PC2 and PC3 reached extremely significant levels (P＜0.01) when detecting population difference, and the traits with higher factor loading were primarily head, dorsal fin, anal fin, and abdomen. The cumulative contribution rate of the four principal component variances in the non-reproductive period was 46.61%, and the scores of PC1 and PC2 reached extremely significant levels (P＜0.01) when detecting population difference. The traits with higher factor loading were primarily head, body height, dorsal/pelvic fins, and anal fin length. The head and trunk traits of the two populations could be differentiated, as the dorsal and anal fins were longer and the upper margin and abdomen were shorter in the south-central East China Sea group than in the Yellow Sea group. This morphological variation may be attributed to the specialization of phenotypic traits induced by migratory life history strategies. The results of this study support the theory that migration behavior and complex habitats improve environmental adaptability, and aid in improving our understanding of the ecological characteristics and evolutionary trends of species.