The ontogenetic changes of the scallop Patinopecten yessoensis from Dalian, China, were studied during four stages (3, 6, 12, and 24 mo) using a geometric morphometric method and cross-validation method for evaluating the utility of the classification. The results showed that they exhibited characteristically different ontogenetic trajectories within a space defined by test size and shell shape. Landmark and semilandmark analyses were applied to successfully determine the stage of the individuals with approximately 89.04% accuracy. Moreover, each stage had a typical shell shape. The distinction of these patterns was assigned to the circularity and symmetry of the disc and the symmetry of the auricles: the 3 mo shells had a circular disc and asymmetrical auricles, and the 6 and 12 mo shells showed a more elongated disc and more symmetrical auricles, whereas the 24 mo shells showed an elongated disc and relatively small, symmetrical auricles. The ontogenetic shell form changes (size + shape) of P. yessoensis reflected the life history characteristics, which could potentially be used for age stage identification. The results provide a reference for determining the growth stage of P. yessoensis during fisheries and aquaculture management.