Morphometric disparities were employed to characterize the geographical variations in and elucidate the phylogeography of Portunus sanguinolentus in East Asia. In this study, a comprehensive assessment was undertaken based on measurements from 833 individual crabs. These crabs were sampled from eight distinct locations, namely Kyushu (KS), Fuzhou (FZ), Yilan (YL), Xiamen (XM), Tainan (TN), Hong Kong (HK), Vietnam (VN), and Singapore (SG). Twelve morphometric measurements were standardized based on size using the allometric method. A cluster analysis and a canonical variate analysis (CVA) were then conducted for a data analysis. Randomization tests were subsequently performed to validate the morphometric differences observed among the groups. The analytical results classified the eight sampled populations into at least two distinct clusters. The first cluster included three samples from China (specifically FZ, XM, and HK), while the second cluster consisted of samples from East Asia (including KS, YL, TN, VN, and SG). The CVA revealed a tripartite division into three groups: the mainland China group (FZ, XM, and HK), the Kuroshio group (KS, YL, and TN), and the Southeast Asia group (VN and SG). The observed morphometric variations between these broad groups were statistically significant for both genders. These differences may be attributed to evolutionary origins, geographical events, or environmental adaptations. This study highlights the effectiveness of morphometric techniques in providing comprehensive insights into species delimitation and philogeographic relationships.