Within the coral reef habitat, members of the Symbiodiniaceae family stand as pivotal symbionts for reef-building corals. However, the physiological response of Symbiodiniaceae on microplastics are still poorly understood. Research conducted in this investigation assessed the harmful impact of polystyrene microparticles (PS-MPs) on Cladocopium goreaui, a Symbiodiniaceae species with a broad distribution. The results showed that micrometre-sized PS-MPs had a greater toxic effect on C. goreaui than nanometre-sized PS-MPs, and the growth inhibition rate of a concentration of 20 mg/L with 10 μm-sized PS-MPs on C. goreaui was as high as 62.9%-86%, which almost completely inhibited cell proliferation. Exposure to 10 μm PS-MPs significantly increased cell damage, for instance, the concentration of extracellular polymeric substance and malondialdehyde have increased by 161.6%-184.4% and 261.8%-896% on days 10-20 respectively. Furthermore, When PS-MPs inhibited the photosynthesis of C. goreaui, it could ensure their typical photosynthetic activity maintained by increasing their chlorophyll levels, and the increase in chlorophyll concentration is proportional to the level of inhibition experienced. However, Exposure to 10 μm PS-MPs could damage the chloroplasts of C. goreaui, leading to a decrease in the ability to synthesize photosynthetic pigments and subsequently resulting in a reduction in photosynthetic capacity. The morphology and genetic activity of C. goreaui suggest that PS-MPs primarily induce cellular shrinkage and distortion, as well as the disintegration and impairment of nuclear and chloroplastic structures, concurrently eliciting a greater number of suppressed genes, predominantly those associated with the function of succinate dehydrogenase, the attachment to tetrapyrroles, the binding of haem, and the handling of iron ions, including activities related to oxidoreduction. The investigation examined the adverse impacts of PS-MPs on a crucial coral symbiont (Symbiodiniaceae) and the beneficial reaction of these algal organisms, enhancing comprehension of how microplastic pollution affects the coral reef ecosystem.