Distant hybridization is an important breeding method in aquaculture. However, hybrid escape is frequent in aquaculture and may have a negative impact on indigenous species. In addition to reducing the fertility of hybrids, inhibiting their wild viability can also play a role in avoiding the ecological risk of escaped hybrids. Postzygotic ecological isolation refers to the phenomenon of reduced adaptation of hybrids in the parent environment (wild), such as the incompatibility between their phenotypes and their behavior or food resources, which suggests that differences in parental feeding habits may also weaken the adaptability of the hybrids in the wild. In this study, we compared external and skeletal traits related to feeding habits in carnivorous Percocypris pingi (PP), herbivorous Schizothorax wangchiachii (SW), their F1 hybrids (PS), and omnivorous S. davidi (SD). Then, we selected fish, shrimp, chironomid larvae, and periphytic algae as food resources corresponding to different ecological niches and carried out a short-term single-food feeding experiment (sufficient food) under monoculture and a 60-day mixed-food feeding experiment (limited food) under polyculture. We found that PS and SD had similar traits, which were intermediate between those of PP and SW. In the single-food experiment, PS and SD had no significant difference in the foraging level of the four food resources, and they showed little foraging for fish and algae. However, SD showed stronger competitive ability than PS under polyculture (feeding chironomid larvae). In the 60-day ecological simulation experiment, PS could barely forage for fish and shrimp, and its ecological niche was close to that of SW. PS did not gain weight during the experiment, which indirectly reflected its low adaptability in the wild. In summary, the concept of postzygotic ecological isolation was introduced into aquaculture for the first time in this study. Moreover, this study also suggests that reducing the ecological risk caused by the escape of transgenic and genome edited varieties can not only by reducing their fertility, but also by reducing their ecological adaptability, which may lead to their elimination at the larval stage in the wild. This provides new insights for the genetic containment of genetically improved varieties.