Microplastics (MPs) have aroused widespread concern due to their extensive distribution in aquatic environments and adverse effects on aquatic organisms. However, the underlying toxicity of different kinds of MPs on freshwater microalgae has not been examined in detail. In this study, we investigated the effects of polyvinyl chloride (PVC), polystyrene (PS) and polyethylene (PE) MPs on the growth of Microcystis aeruginosa, as well as on its toxin production and oxidative stress. We found that all three kinds of MPs had an obvious inhibition effect on the growth of M. aeruginosa. Considering the results of antioxidant-related indicators, the activity of superoxide dismutase (SOD) and catalase (CAT), and cell membrane integrity were greatly affected with exposure to PVC, PS and PE MPs. Moreover, the content of intracellular (intra-) and extracellular (extra-) microcystins (MCs) had a noticeable increase due to the presence of PVC, PS, and PE MPs. Finally, according to the comprehensive stress resistance indicators, the resistance of M. aeruginosa to three MPs followed the order: PE (3.701)> PS (3.607)> PVC (2.901). Our results provide insights into the effects of different kinds of MPs on freshwater algae and provide valuable data for risk assessment of different types of MPs.