Due to increasingly severe microplastic pollution in freshwaters, the interaction between these contaminants and cyanobacteria warrants study. In this study, we expose the freshwater cyanobacterium Microcystis aeruginosa to different sizes (1 μm and 100 nm) of polystyrene (PS) microplastics of 5 mg/L. Results indicate 1 μm microplastics promote algal growth (12.42% ± 0.94%) at 96 h, and have greater potential to aggregate on algal cell surfaces and inhibit photosynthesis. But no significance was observed in 100 nm microplastics treatment on algal growth and photosynthetic activity after 96 h exposure. Especially, 1 μm microplastics increased the content of intracellular microcystins (MCs) (18.42% ±0.33%) after 72 h and inhibit MCs release (23.87% ±8.79%) at 72 h, while 100 nm PS microplastics promote MCs production only at 48 h (14.83% ± 7.07%). Results indicate that smaller size does not necessarily mean greater toxicity, 1 μm microplastics showing more adverse effects than 100 nm microplastics to M. aeruginosa, improving understanding of the toxicity of microplastics in freshwater ecosystems, and challenging the conventionally held belief that smaller microplastics are more toxic.