This research was conducted to explore the morphological characteristics and difference of Saurogobio dabryi in different river sections of Jialing River. A total of 120 samples collected from upstream, midstream and downstream of Jialing River were analyzed, using the multivariate morphometric method and the landmark-based geometric morphometric method. The morphometric analysis illustrated that there were significant differences among populations of S. dabryi in different river sections. The morphological variations of the three populations were mainly observed on the head, fin and caudal peduncle. The body of S. dabryi in the upstream group was the most slender. Besides that, the fork length, length between pectoral fin and ventral fin, trunk length, the inter-orbital width, dorsal fin coxal length, head depth and beard length in this group were the largest. The midstream group of S. dabryi had the longest pectoral fin, ventral fin and caudal fin, the strongest caudal peduncle, the largest of the width of caudal stalk, the depth of caudal stalk, the longest head, the widest body and the largest length between pectoral fin and rhynchodaeum. For S. dabryi in the downstream, the length between anus and anal fin and head width of the lower reaches were the largest. However, the scatter diagram of relative warp scores analysis showed that S. dabryi population from different river sections of Jialing River cannot be distinguished. The variation coefficient of morphometric characters showed that the phenotypic differences of S. dabryi in the three river sections were intraspecific. We speculated that the morphological variations of S. dabryi in Jialing River should be the result of adaptive evolution to the diverse environments in Jialing River, such as the flow rate, water temperatures, and food types.