Otolith chemical signatures are sufficiently stable across time to allow for accurate stock classification. The classification of the southern Yellow Sea population for Larimichthys polyactis (Bleeker, 1877) and its connectivity with others from 1962 is controversial. The study aimed to study the inter-annual variation in otolith strontium:calcium (Sr:Ca) ratios of L. polyactis to determine whether otolith natural tags are representative over long periods and can then be used for population structure classification. Spawning L. polyactis individuals were captured by stow nets in the same site of the southern Yellow Sea coastal waters during April–May in 2003, 2012, and 2013. EPMA (electron probe microanalysis) was used to determine the Sr:Ca ratios of a total of 25 otolith samples. Mann–Whitney U-test was used to test the differences of otolith Sr:Ca ratios from the core to edge for each otolith. One-way ANOVA was performed to compare the mean otolith Sr:Ca values among 2003, 2012, and 2013. Otoliths from 2003, 2012, and 2013 showed similar patterns of Sr:Ca ratios and Sr:Ca ratios could be divided into higher and lower phases in the core and remaining regions, respectively. Inter-annual significant differences for each high or low Sr:Ca phase of otoliths were not observed over short- (between 2012 and 2013) or long-time (between 2003 and 2012, and between 2003 and 2013) scales. Univariate contrasts across the adjacent year and decade classes were statistically similar. The Sr:Ca ratio signatures in the otolith were relatively stable across years and can be used as a reliable natural tag for connectivity assessments and stock identification with little or no genetic differentiation among L. polyactis populations. The short- and long-term temporal stability of otolith Sr:Ca ratios also revealed, the existence of stable L. polyactis stocks in the southern Yellow Sea, consistent with a previous finding of capture survey.