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Microplastics (MPs) have been proven to be one of the major threats to the wastewater treatment system. However, the impact of MPs on microalgae-based wastewater treatment technology are still unknown. In this study, effects of polyvinyl chloride (PVC), polypropylene (PP), and polyethylene (PE) on the removal of nitrogen and phosphorus from synthetic piggery digestate by microalgae were investigated. Results show that the effect of PVC particle size on the growth of microalgae was significant. The effects of PVC content, PP particle size and content, PET particle size and content on the growth of microalgae were all not significant. The removal of ammonia nitrogen by microalgae was influenced significantly by PVC particle size and content, PP particle size and content, the effects of PET particle size and content on the removal of ammonia nitrogen were all not significant. The effects of particle size and content for three MPs on the removal of total phosphorus were all significant. Microalgae cells were bound together after being adsorbed by MPs, which increased the secretion of extracellular polymers and influenced the removal of ammonia nitrogen and total phosphorus.