As one of the top four commercially important species in China, yellow croaker (Larimichthys polyactis) with two geographic subpopulations, has undergone profound changes during the last several decades. It is widely comprehended that understanding its population dynamics is critically important for sustainable management of this valuable fishery in China. The only two existing population dynamics models assessed the population of yellow croaker using short time-series data, without considering geographical variations. In this study, Bayesian models with and without hierarchical subpopulation structure were developed to explore the spatial heterogeneity of the population dynamics of yellow croaker from 1968 to 2015. Alternative hypotheses were constructed to test potential temporal patterns in yellow croaker’s population dynamics. Substantial variations in population dynamics characteristics among space and time were found through this study. The population growth rate was revealed to increase since the late 1980s, and the catchability increased more than twice from 1981 to 2015. The East China Sea’s subpopulation witnesses faster growth, but suffers from higher fishing pressure than that in the Bohai Sea and Yellow Sea. The global population and two subpopulations all have high risks of overfishing and being overfished according to the MSY-based reference points in recent years. More conservative management strategies with subpopulation considerations are imperative for the fishery management of yellow croaker in China. The methodology developed in this study could also be applied to the stock assessment and fishery management of other species, especially for those species with large spatial heterogeneity data.