Abstract: To investigate the effects of saline-alkaline stress on the intestinal tract of naked carp (Gymnocypris przewalskii), first-year naked carps weighing (8.13±1.45) g were domesticated in different stress conditions at a water temperature of (15.3±1.6)℃ for 28 d. The stress groups included a salinity stress group (Y100), an alkalinity stress group (J100), and a mixed saline-alkaline stress group (YJ100), with 3‰ salinity serving as the control group (CK). The results showed that the pH value was the highest in J100 group and the lowest in CK group, while the ammonia nitrogen content was the highest in Y100 group and the lowest in YJ100 group. The intestinal structure of Gymnocypris przewalskii in the Y100 group was more complete than that of the other groups, characterized by the intact plasma membrane layer and well-developed striated margin. On the contrary, the foregut of the naked carp in the J100 and YJ100 groups was damaged, with the thickness of the muscularis propria decreasing progressively from the foregut to the hindgut. In the CK and Y100 groups, the foregut showed the highest wrinkle height, followed by the midgut and the hindgut, while the opposite pattern was observed in the YJ100 group. In the J100 group, the midgut exhibited the highest wrinkle height, followed by the hindgut, with the foregut being the lowest. Furthermore, the midgut showed higher expression levels of osmosis-related genes, including GpAQP1, GpMAPK14, GpPLA2, and GpCA2 under different stress conditions, whereas the foregut exhibited high expression of GpNKA1 and GpALP. In conclusion, saline and alkaline treatments caused damage to the intestinal structure of Gymnocypris przewalskii, thus affecting the growth and development of the fish. This finding provides insights into the slow growth observed in Gymnocypris przewalskii exposed to saline-alkaline stress in natural habitats.