We have sampled 194 Schizothorax nukiangensis, 152 Ptychobarbus kaznakovi and 117 Schizopygopsis thermalis in Tibet section of the Nujiang River between May and October 2017 (Fig. 1, 2; Table 2) in order to compare the morphological characteristics of digestive organs including feeding and digestive organs among the three Schizothoracinae fish species. Three methods of multivariate analysis were applied to analyze the morphological difference of feeding and digestive organs. The results showed that major parts of interspecific variation were the cephalic and enteral characteristics (Fig. 3, 4; Table 5, 6), and the morphological indexes of different species were significantly different among the three species (P < 0.05) (Table 3). The cephalic morphology of the three species was with differences. Analysis on the enteral inclusion under microscopes was applied to understand their food competition. The results indicated that Schizothorax nukiangensis and Ptychobarbus kaznakovi belonged to the omnivore and partial carnivore fish (Fig. 6), and the Schoener overlap index between two species was high (0.91). Schizopygopsis thermalis belonged to the omnivore and partial herbivore fish. The indexes of diversity of dietary composition among three species of fishes were apparently different (Table 8). Feeding habits of the three fishes were closely related to environmental factors, such as water temperature, flow rate and altitude (Table 1).