The potential of microplastics (MPs) to act as carriers for contaminants or engineered nanomaterials is of rising concern. However, directly determining the vector effect of polystyrene (PS) MPs towards nano-hydroxyapatite (nHAP) particles, a typical nano phosphorus fertilizer and soil remediation material, has been rarely studied. In this study, the interaction of differentially surface functionalized PS MPs with nHAP were investigated through batch experiments under different solution chemistry conditions. The results demonstrated that nHAP had the highest attachment/adsorption affinity onto carboxyl-functionalized PS, followed by bare PS and amino-functionalized PS under near-neutral pH conditions. Adsorption of nHAP exhibited a strong pH-dependent behavior with PS MPs, increasing under acidic-neutral pH (3−7) and decreasing at higher pH values. The presence of humic acid and NaCl hindered the adsorption of nHAP onto MPs. Scanning electron microscopy observations revealed a rod-like morphology for adsorbed nHAP, which was randomly distributed on MPs surface. Surface complexation and cation-π interaction were mainly responsible for the adsorption of nHAP as revealed by multiple spectroscopic analyses. These results provide mechanistic insights into nHAP-PS interactions and expound the effect of surface functionalization of PS on binding mechanisms, and thus bring important clues for better understanding the vector effects of MPs towards nanoparticles.