In this study, 11 normal characters and 16 frame traits had been measured in 89 Pseudorasbora parva among different geographical populations (Zhenyuan, Mojiang and Jiangcheng) from Lixianjiang, Red River drainage. These data were analyzed by three different methods, the principal component analysis (PCA), the discriminant analysis and the coefficient of difference analysis to compare the morphological differences among the three geographical populations of P. parva. The results showed that Zhenyuan population was independent from the other populations. In PCA analysis, the contribution rates of PC1, PC2 and PC3 were 55.094%, 8.397%, and 6.988% respectively, and cumulatively to 70.469%. Furthermore, largely independent samples in Zhenyuan were separated in the scatter plot results by the PC1 and PC2. Also in the discriminant analysis, the discriminant rate based on 7 characters variable (P<0.01) reached 100% in Zhenyuan populations, while 96.7% both in Mojiang and Jiangcheng populations. Then, the same 7 traits with body length ratio were used for coefficient of difference analysis, and it was found that both with 3 characters with the more difference coefficient than 1.28 between Jiangcheng and Zhenyuan, Mojiang and Zhenyuan populations. It is speculated that there are morphological variations in Zhenyuan P. parva. Except the real source of the P. parva, environmental factors, genetic factors may also play a significant role in morphological variation. Therefore, it is necessary to study it by means of molecular biology in future.