To explore the morphological differences among geographically distinct populations of Gymnodiptychus dybowskii and the evolutionary mechanisms underlying their differentiation, 87 samples were collected from the Kaidu River, Turks River, Emin River, and Manas River in Xinjiang between 2020 and 2021. Classic fish ecology research methods, including traditional morphometrics and frame measurement, were used to analyze their morphological characteristics. One-way ANOVA detected significant inter-population differences in 13 proportional morphological traits (p < 0.01) and an additional 3 traits (p < 0.05) among the 34 traits examined. The most divergent traits were primarily concentrated in body width, snout length, mouth gape, caudal peduncle length, and various fin dimensions. The first three principal components extracted via PCA cumulatively accounted for 61.34% of the total variance. PC1 primarily reflected variation in overall body size and trunk elongation, while PC2 captured morphological differentiation linked to adaptation to distinct environmental conditions. A discriminant function model built on seven key traits achieved an overall correct classification rate of 94.3% for the four geographic populations. This study confirms that G. dybowskii populations across different hydrological gradients have undergone significant morphological divergence, with observed patterns closely linked to local environmental adaptation. These findings provide a critical morphological foundation for understanding the phenotypic evolution of this plateau-endemic fish and inform its adaptive management strategies.