In this study, gut microorganisms of herbivorous grass carp, omnivorous carp, crucian carp, and aquatic microorganisms were collected from natural salt–alkali lakes and ponds in Xinjiang in winter to analyze their community structures. We sequenced 16S rRNA amplicons to investigate the composition and function of the microorganisms in the gut. PCoA analysis revealed that the gut microbiota of herbivorous and omnivorous fish formed two distinct clusters. Proteobacteria, Actinobacteria, Desulfobacterota, Firmicutes, and Chloroflexia are the dominant bacteria in the gut of fish. Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Gram-negative bacteria are the dominant bacteria in the water. Carbohydrate- and protein-degrading bacteria, such as Desulfofustis, Lactiplantibacillus, and Vibrio, were predominant in omnivorous fish (CC and GRC), while cold-resistant bacteria, such as Shewanella and Psychromonas, were colonized in grass carp. This suggests that the same environment does not lead to similar gut bacteria, and that specific endogenous factors play a far more important role in shaping the microbiota composition than environmental factors.