Abstract: Shell traits play an important role in the identification and delimitation of mollusk species. Determining the growth stage of Pecten is always a challenge in aquaculture, taxonomy, and evolution. In order to explore the morphological differences of the scallops cultured in the offshore deep-water sea area and the inshore shallow water sea area, traditional morphometry and geometrical morphometry methods were used to obtain their morphological differences. We tested the variation in shape indexes between the two groups of different water depth using the Independent-samples T test. For geometric morphometric analysis, we performed generalized procrustes analysis (GPA) on the collected morphological data coordinates of the two scallops. Then we subjected transformation data to principal component analysis (PCA) and canonical variate analysis (CVA). The results of the traditional multivariate morphometric analysis showed that the shell height (SH), shell length (SL) and shell width (SW) of the scallops in the deep water were significantly larger than the scallops in the shallow water (P<0.01); Through the analysis of landmarks and semi-landmarks variations, the results showed that the overall shell size of the scallops in the deep water was larger than that of the scallops in the shallow water and there is a significant difference in the auricles and disc of the two scallops after removing the size factor. This paper not only provides a theoretical basis for morphological research for the deep-water aquaculture of the scallops, but also providing a reference for selecting appropriate methods in the morphometric research.