The wide coverage of the north and south seas of China makes the ecological environment geographically different. Octopus minor inhabiting different sea areas thus formed corresponding apparent differences in morphology. A multi-variate analysis method including the principal component analysis, discriminant analysis, One-Way ANOVA and stepwise discriminant analysis was used to comprehensively analyze the 14 morphological indexes of 11 natural O. minor populations along the coasts of China and a population discriminant function was established. The results showed that the arm formula of O. minor was 1 > 2 > 3 > 4 and the web formula was A > B > C > D > E. Principal component analysis showed two principal components were constructed with a cumulative contribution rate of 66.067%. The first principal component included the MW/TL, HW/TL and FFL/TL, with their contribution rate of 36.979%, while the second principal component contained the TWt/TL, ML/TL and FL/TL with the contributory rate of 29.088%. Importantly, the Penghu group can be clearly distinguished based on the scatter plots of principal component analysis. The integrative discrimination accuracy was 60.400% based on the discriminant functions. One-Way analysis of variance (ANOVA) implied that there are significant differences between the number of suckers in the arms of Penghu and the other populations. The cluster analysis revealed that five northern populations and the Yilan population grouped together at first, then clustered with Shengsi, Nanjidao and Lianjiang, then finally clustered with Penghu, while Quangang formed into a separated group. All of those indicated that five northern populations showed high morphological similarity while it was not the case for the southern populations. And there are significant variations between the northern and southern populations. Especially Penghu and Quangang populations exhibited/showed relatively large differences with the others. In summary, eleven O. minor populations in the coastal Chinese sea exhibited significant morphological divergence, and the morphological diversity was relatively high.