Microcystis blooms are generally associated with zooplankton shifts by disturbing interspecific relationships. The influence of Microcystis on competitive dominance by different sized zooplanktons showed species-specific dependence. We evaluated the competitive responses of small Moina micrura and large Daphnia similoides to the presence of Microcystis using mixed diets comprising 0%, 20%, and 35% of toxic M. aeruginosa, and the rest of green alga Chlorella pyrenoidosa. No competitive exclusion occurred for the two species under the tested diet combinations. In the absence of M. aeruginosa, the biomasses of the two cladocerans were decreased by the competition between them. However, the Daphnia was less inhibited with the higher biomass, suggesting the competitive dominance of Daphnia. M. aeruginosa treatment suppressed the population growths of the two cladocerans, with the reduced carrying capacities. Nonetheless, the population inhibition of Daphnia by competition was alleviated by the increased Microcystis proportion in diet. As a result, the competitive advantage of Daphnia became more pronounced, as indicated by the higher Daphnia: Moina biomass ratio with increased Microcystis proportions. These results suggested that M. aeruginosa strengthens the advantage of D. similoides in competition with M. micrura, which contributes to the diversified zooplankton shifts observed in fields during cyanobacteria blooms.