The Japanese Spanish mackerel Scomberomorus niphonius (Cuvier, 1832) is widely distributed in the subtropical and temperate waters of the northwestern Pacific Ocean, supporting one of the most important commercial fisheries in China. However, ignoring the potential population structure changes induced by fishing pressure and climate change may undermine the population stability under the current management strategy. In this study, the population structure of the Japanese Spanish mackerel was investigated based on a morphometric truss network system. A total of 534 individuals were randomly collected from commercial gill nets spanning eight major spawning grounds in the Bohai, Yellow, and East China Seas during the peak spawning seasons respectively. A total of 17 measurements (including eye diameter) were conducted in each specimen and subjected to principal component analysis (PCA) and discriminant function analysis (DFA). The results of PCA indicated that the first two factors cumulatively caused 78.38% of the total morphometric variation and observable differences, primarily fin the caudal and trunk areas. The results of DFA revealed that the eight spawning groups can be divided into three stocks, i.e., southern, middle, and northern stocks, with 68.7% of total accuracy. In contrast to previous studies, the spawning groups of the Japanese Spanish mackerel demonstrated a tendency to disperse to northern regions. In conclusion, this study found that to maintain the stability of the population structure and the total production of Japanese Spanish mackerel S. niphonius (Cuvier, 1832), a newly revised management method should be developed and implemented.