In this study, we employed geometric morphometrics (GMs) to analyze the shell shape differences among two mass-selected strains of bay scallops (red shell strain (RS) and black shell strain (BS)) and a control group (CG). The results revealed distinct shell shape differences corresponding to shell coloration, with the black shell strain displaying a more elliptical shell compared to the red shell strain. Additionally, the umbonal angle of the red shell strain was smaller than that of the black shell strain, indicating that the black shell strain had a more favorable jet direction that could enhance swimming capabilities. To evaluate the model’s performance in practical applications, leave-one-out cross-validation was carried out on the two shell strains and one control group. The results demonstrated discrimination accuracy rates of 67.44%, 47.62%, and 68.18% for the BS strain, RS strain, and CG, respectively. Similarly, for the right valves, the discrimination accuracy rates were 62.79%, 50.00%, and 75.00% for the BS strain, RS strain, and CG, respectively.