Microplastics (MPs) and per- and poly-fluoroalkyl substances extensively coexist in aquatic environments and potentially endanger organisms. Microalgae may decrease the effective concentration of pollutants via hetero-aggregation with MPs and adsorption of emerging contaminants. However, the potential influence of coexistent pollutants on hetero-aggregation of MPs and microalgae remains unknown. This study investigated the hetero-aggregation process involving different sizes of polystyrene (PS, 3.0 and 50.0 μm) with Chlorella sorokiniana (C. sorokiniana) in the presence or absence of perfluorobutanoic acid (PFBA) along settling experiments, scanning electron microscope, and Derjaguin-Landau-Verwey-Overbeek (DLVO) model. We found that the hetero-aggregation between C. sorokiniana and 3 μm PS was more pronounced than with 50 μm PS, while PFBA inhibited this process. ΔOD1 values (reflected hetero-aggregation level) for 3PS-cells and 50PS-cells were 0.189 and 0.087, respectively, and PFBA decreased these values to 0.134 and 0.033. Furthermore, extracellular polymeric substances, known as inducer of hetero-aggregation, increased by 14.33% when exposed to 3 μm PS alone, whereas the co-exposure group showed a decrease of 4.52% compared to 3PS-cells group. PFBA also significantly decreased the protein/polysaccharide ratios in both MPs sizes, reducing hetero-aggregation. DLVO theory revealed that microalgae lowered the energy barrier significantly, while PFBA elevated it, indicating that hetero-aggregation was inhibited by PFBA. This study provides new perspectives for pollutant removal and toxicity variation in aquatic environments.