There is a strong coupling between benthic and pelagic habitats in shallow aquatic ecosystems. The outcomes of the coupling determine the key characteristics of these systems. The competition between benthic and pelagic algae for light and nutrient is one of the most important ecological processes of benthic-pelagic habitat coupling in shallow freshwater ecosystems when macrophytes are absent. However, the coupling is affected by omnivorous fish. This minireview first focuses on the coupling of benthic-pelagic habitats in shallow aquatic ecosystems in general. Then we review how omnivorous fish affect the benthic-pelagic interactions. Generally, omnivorous fish may increase water nutrient levels, enhance pelagic algae growth, reduce water clarity, and limit the growth of benthic algae, thereby accelerating the eutrophication process in shallow aquatic ecosystems. However, the mechanisms and overall effect differ among different fish species depending on whether their diet is benthic omnivore, plant-based, or animal-based omnivore. In addition, fish size and age also play a role. The proportion of the omnivorous fish biomass tends to increase with increasing human impact, such as fish stocking, eutrophication, and global warming, therefore, the effects of omnivorous fish on aquatic ecosystem are increasing, far-reaching, and deserve continuous attention.