Cyanobacterial blooms are an increasing problem in a more eutrophic world. It is still a challenge to fully understand the influence of cyanobacteria on the interactions between predator and prey at higher trophic levels. The present study was mainly undertaken to understand the inducible anti-predator responses of cladocerans while using cyanobacteria as part of food. Specifically speaking, we focused on the anti-predator strategies of Ceriodaphnia cornuta in response to different predators (fish and Chaoborus larvae) under food with different proportions of Microcystis aeruginosa. The morphological (i.e., body size and the induction of horns) and life history traits (e.g., time to first reproduction, offspring number, and survival time) responses were measured under different proportions of M. aeruginosa (i.e., 0%, 20%, 40%, 60%, 80%, and 100%). Our results showed that both the life history and the inducible anti-predator responses of C. cornuta were significantly affected by different concentrations of M. aeruginosa. Specifically, lower concentrations of Microcystis (20%–60%) can significantly promote the horns induction under Chaoborus predation risks, and higher Microcystis concentrations (60%–100%) tend to enhance reproduction in response to fish predation risks, such as larger body size, decreased time to first reproduction, and increased total offspring number. Additionally, an increasing concentration of M. aeruginosa decreased the ability of C. cornuta to reverse horns when predation risks removed. Our findings indicated that cyanobacteria affecting life history traits and the subsequent indirect effects on anti-predator responses in cladocerans could impact the interactions between predator and prey at higher trophic levels and may consequently contribute to shaping the structure of the community in a cyanobacteria bloom area.