Nanoplastics (NPs) pollution has become an emerging threat to the aquatic environment and its organisms. The removal of NPs from contaminated water is a global challenge. In this study, an efficient and reusable composite was prepared from cetyltrimethylammonium bromide (CTAB) modified magnetic biochar. The performances of CTAB modified magnetic biochar (CMB) to remove polystyrene (PS) and carboxylate-modified polystyrene (CPS) nanoparticles from water were systematically evaluated. The results showed that the PS and CPS removal performance of magnetic biochar was improved by CTAB modification. These increases were assigned to the increase in the surface hydrophobicity of CMB. Due to the strong electrostatic repulsion between the nanoparticles, PS and CPS maintained high stability in alkaline conditions, resulting in a significant decrease in removal efficiency. The removal efficiency was decreased to 67.4% for PS and to 40.7% for CPS at pH 11. The inhibition effects of NaCl on the PS and CPS removal efficiencies were decreased gradually with the increase of NaCl concentration. Among the anions studied, H2PO4− had the biggest impact on the removal performance of CMB. Besides, CMB could be used to remove PS and CPS in real surface water, and the removal efficiencies of PS and CPS were 95.3% and 97.8%, respectively. Particularly, the removal efficiencies of PS and CPS were 90.2% for PS and 94.8% for CPS when CMB was recycled five times. According to the characterization results of XRD, TGA, SEM, FTIR and XPS, PS and CPS nanoparticles were removed by CMB from water mainly through aggregation instead of adsorption. The efficient removal of PS and CPS by CMB via aggregation process offers new insight into the removal of NPs from aquatic environment.