Micro- and nano-plastics (MNPs) are increasingly prevalent pollutants in marine ecosystems and result in various deleterious effects on marine organisms. There have been studies evaluated the toxic effects of MNPs on marine microalgae, but few of them focused on the effects of MNPs on dinoflagellate species and their toxins production, which could have significant implications on human health and ecological safety in coastal areas. In this study, the common harmful algal blooms-causing dinoflagellate Alexandrium tamarense was exposed to 0.1 and 1 μm sized polystyrene nanoplastics (NPs) to investigate the responding patterns of population growth, multiple physiological functions, as well as the intracellular paralytic shellfish toxins (PSTs) productions. The results indicated the population growth, photosynthetic parameters, nutrients (nitrate and phosphate) uptake rates and extracellular carbonic anhydrase activities (CAext) were all inhibited by the two sized NPs, accompanied by the prolonged and more aggregated microalgal cells under the observation of scanning electron microscope (SEM), and the inhibition effects were more severe under 1 μm sized NPs than 0.1 μm sized NPs. Finally, we found the intracellular PSTs contents increased 73.59% exposed to 0.1 μm sized NPs while decreased 85.50% exposed to 1 μm sized NPs comparing the controls at 96 h, without significant changes of relative compositions. These results provided evidence that MNPs were toxic to A. tamarense and affected their intracellular PSTs productions within 96 h, which is critical to consider when evaluating the potential risks of MNPs in marine ecosystems.