The morphological variations among different populations of Coilia nasus, collected from the south branch (NZ) and north branch (BZ) of the Yangtze Estuary, Neihe of Chongming (NH) and Shengsi (SS) in Zhejiang Province, were assessed to determine the population compositions using traditional morphology and the truss network model. All morphological variable data were analyzed using multivariate statistical approaches, such as one-way analysis of variance (ANOVA), principal component analysis (PCA), discriminate function analysis (DFA), and cluster analysis (CA). ANOVA revealed significant differences in all morphological variables among the groups, except head length behind the eyes, tail length, the dorsal origin of the caudal fin-origin of the pelvic fin, termination of the anal fin-origin of the anal fin, the origin of the anal fin-origin of the pelvic fin, and end of operculum-end of operculum (P＜0.05). Based on the coefficient of variation (CV), the morphological variation among different C. nasus populations in the Yangtze Estuary was very small. The differences among the groups were mainly due to differences in the lateral trunk and head length. The lateral trunk was the primary variation axis, while the head length was the secondary variation axis. The stepwise discriminant comprehensive rate was 80.60%, and the cross-validated comprehensive discriminant rate was 76.30%. The BZ group had the best discrimination accuracy rate (95%), indicating the best discriminant effect, while the NH group had the lowest discrimination accuracy. According to the CA results, the four populations can be divided into three groups: Group I, the NZ and NH populations; group II, the SS population; and group III, the BZ population. The results of CA were similar to those of DFA, indicating the homogeneity and heterogeneity of the population differences. The lateral trunk and head length were identified as the main differences among the different populations of C. nasus in the Yangtze Estuary, which may be caused by differences in diet and habitat use.