【Objective】 To explore the analysis of differences in morphological characteristics of Gymnodiptychus dybowskii of different geographical populations. 【Methods】 From 2020 to 2021,Gymnodiptychus dybowskii were collected from Manas River and Turks River, fish ecology was used to identify its morphological characteristics and analyze their different population biological traits. 【Result】 The differences in appearance characteristics between Manas River group and Turks River group of Gymnodiptychus dybowskii were more obvious, and the differences in body weight and body length between the two groups were significant (P<0.05), body width and head length, range and mean values in Manas River and Turks River were significantly different (P<0.01. Regression equation of body length and body weight: WM=0.049L1.992 8(R2=0.932,0),WT=1.39×10-6L3.127 5(R2=0.964,8).The growth trends of biological traits in different populations of Gymnodiptychus dybowskii were different: the head length of Manas River population was obvious, while that of Turks River population was body width. Combined with the Manas River population of 35 and the Turks River population of 65, the principal component 1 was 54.6%, and the principal component 2 was 11.6%. There was no overlap between either population; The main traits affecting principal component 1 were: body height, dorsal fin starting point to ventral fin starting point; The main traits affecting principal component 2 are: dorsal fin starting point to dorsal fin posterior base, dorsal fin starting point to hip fin starting point, dorsal fin starting point to caudal fin. The Manas River group and the Turks River group could be distinguished according to their shapes, and their functions are as follows: YM = -1,985.90-1,934.51X1-2,020.77X2 + 5,137.86X3 + 2,858.24X4 + 3,111.14X5-2,376.61X6 + 2,494.94X7 + 4,382.91X8; YT = -1,826.92-2,036.21X1-1,770.91X2 + 4,898.46X3 + 3,679.48X4 + 1,882.97X5-919.60X6 + 3,189.76X7 + 4,632.12X8. The growth traits body height, tongue length and eye cross were directly influential growth factors in the life history of Gymnodiptychus dybowskii and played a key role in guiding their selection and breeding. 【Conclusion】 Gymnodiptychus dybowskii,a common species in the north-south water system of the Tianshan Mountains, highly specialized fish, is extremely important for the diversity of water ecological environment, with widely varying morphological characters, typical heterogeneous plateau fishes, heterogeneous growth rates and instability, and obvious differences in growth traits among different groups, resource depletion has intensified, and there is an urgent need to carry out germplasm restoration and conservation to consolidate the ecological balance of Xinjiang's endemic fishery resources.