Abstract: The water chestnut, known as the fruit of the Trapa species (Lythraceae), is a valuable aquatic vegetable in the Yangtze River Basin, because of its rich mineral composition and high starch content. Fruit morphology is also crucial to manually select Trapa germplasm. However, it is lacking in the different fruit morphologies related to the edible traits. This study aims to investigate the fruit morphology among different Trapa cultivars on the edible traits. 409 Trapa natans (T. natans) germplasm resources were used, including 263 cultivated (a total of 7 varieties) and 146 wild. All fruits were labeled and then imaged in the frontal view. Morphometric measurement and landmark-based geometric profiles were employed to quantify the size and shape of each fruit. Principal component analysis (PCA) and one-way analysis of variance (ANOVA) were conducted to compare the fruit morphological and edible traits among different cultivars. Additionally, Pearson correlation coefficients were calculated to analyze the relationships between fruit morphological and edible traits. The results showed that the fruit length and height of cultivated T. natans were significantly larger than those of the wild, although no significant differences were observed in the fruit width or shoulder angle length. The shell thickness of cultivated T. natans was also significantly greater than that of wild. The two groups occupied distinct regions in the morphological shape space. Principal component 1 (PC1) and principal component 2 (PC2) explained 47.45% and 26.65% of the shape variation, respectively. PC1 primarily reflected the curvature of the shoulder angles, while PC2 represented the sharpness of the shoulder angles. The PC1 values of cultivated T. natans were significantly higher than that of wild, whereas the PC2 values showed the opposite trend. The shoulder angles of cultivated T. natans were more curved, compared with the wild. While the shoulder angles of wild T. natans were sharper than those of the wild. In terms of the edible traits, the single fruit, kernel, and shell weight of cultivated T. natans were approximately 5, 5, and 4 times greater than those of the wild, respectively. The kernel ratio of cultivated T. natans was 65.07%, which was 14.04% higher than that of wild. Significant differences in the fruit morphology and edible traits were observed among the cultivars of T. natans. In fruit size, Erjiaoqingling and Wuling shared the longer fruits, while Sijiaohongling and Huntunling exhibited the wider fruits, and Hongxiuxie and Wuling had the taller fruits. In edible traits, Hongxiuxie and Wuling exhibited the highest single fruit weight, both approximately 10.0 g, while Huntunling and Wuling had the highest and lowest kernel ratio, respectively. In shoulder angle morphology, Hongxiuxie had the least curved shoulder angles, Wuling had the most curved shoulder angles, and Nanhuling had obtuse shoulder angles with almost no prominent protrusions. In shell thickness, Huntunling and Erjiaohongling had thinner shells, while Hongxiuxie and Wuling had thicker shells. Additionally, no negative correlation was observed between shell thickness and kernel weight among all cultivars. Correlation analysis between fruit morphology and edible traits revealed that the kernel ratio was significantly negatively correlated with the shell thickness, shoulder angle length, shoulder angle curvature, and shoulder angle sharpness. The weight components of the fruit (single fruit weight, kernel weight, and shell weight) showed significant positive correlations with the fruit length, fruit width, fruit height, shell thickness, shoulder angle length, and shoulder angle curvature. While there were significant negative correlations with the shoulder angle degree, spine number, and shoulder angle sharpness. In summary, manual selection has significantly altered the fruit morphology and edible traits of T. natans. The cultivars Hongxiuxie, Huntun Ling, and Nanhu Ling were identified as more suitable for further breeding, compared with the rest. These findings can provide important theoretical foundations for the future breeding T. natans.