In this study, we integrated two data systems (morphological analysis and box-truss analysis) to investigate the morphological differences of Schizothorax curvilabiatus among different geographic populations. Multivariate statistical analyses were conducted on 62 morphological parameters collected from three geographic populations in the Yarlung Zangbo River (specifically the Motuo region), Palong River, and Chayu River. The analysis of morphological data revealed that the primary differences among the three populations were evident in several traits, including beard length, head length behind the eye, body height, tail stalk length and thickness, dorsal spine length, and anal fin length. Principal component analysis indicated significant differences in principal component 1 between the Motuo (MT) and Chayu (CY) populations, primarily reflecting characteristics of the head, dorsal fin spine, and tail stalk. Furthermore, box-truss analysis demonstrated significant differences in principal component 1 between the MT and Palong (PL) populations, specifically regarding the head, dorsal fin, central axis, and caudal stalk. In total, 14 and 6 key parameters were selected from the morphological and box-truss data, respectively, to establish discrimination formulas, resulting in initial discrimination success rates of 94.70% and 86.40%. Scatter plots generated from both data systems showed separation by centroid, with the MT population being relatively independent, while the PL and CY populations exhibited some overlap. The cluster analysis revealed that the MT population formed a distinct branch, while the PL and CY populations were clustered. Ultimately, these findings indicated that the morphological characteristics of the MT population are significantly distinct from those of the PL and CY populations, which exhibit minor differences but do not qualify as subspecies.