Recovery of submerged macrophytes has been considered a key factor in the restoration of shallow eutrophic lakes. However, in some subtropical restored lakes, small omnivorous fish dominate the fish assemblages after fish manipulation, and feed in part on submerged macrophytes. Knowledge of the effects of small omnivores on water quality, community structure of plankton, growth of submerged macrophytes, and the stoichiometry of macrophytes is scarce. We conducted mesocosm experiments to elucidated the roles of a small omnivorous bitterling fish (Acheilognathus macropterus) in lake restoration. Our findings indicated that bitterling fish significantly increase nutrient concentrations in the water, mainly through excretion as it had no significant impacts on sediment resuspension. Bitterling fish enhanced the proliferation of phytoplankton, and facilitated the dominance of cyanobacteria, rotifers, and Limnodrilus, in the absence of submerged macrophyte. In a grazing experiment, we found that the growth of four submerged macrophytes to the presence of bitterling fish was species-specific. Bitterling fish selectively grazed on Ceratophyllum demersum, while enhance the biomass percentage of Hydrilla verticillata and Vallisneria denseserrulata. In addition, in a fish excreta experiment, we found that nutrients recycled by the bitterling fish facilitate the growth and change the stoichiometric contents of V. denseserrulata. Our results imply that small omnivorous fish may benefit the development of the meadow-forming V. denseserrulata in subtropical lakes, thus control of omnivorous fish after lake restoration should be species and size re-considered.