Effects of metal ions on the adsorption of organic pollutants have drawn great interests considering their coexistence and interactions in aqueous solution. However, the potential influencing mechanisms of metal ions on the adsorption of organic pollutants at a molecular level were rarely studied. Here, we investigated the effects of Cu(II) on the adsorption of 17 beta-estradiol (E2) and sulfamethoxazole (SMX) by carboxylic and amino CNTs/CoFe2O4 composites, and the mechanisms were revealed by spectroscopy analyses and density functional theory (DFT) calculations. The results showed distinct effects of Cu(II) on SMX and E2 adsorption by CNTs/CoFe2O4. For E2, a nonionic chemical, Cu(II) slightly inhibited E2 adsorption by CNTs/CoFe2O4 due to the increased aggregation of the composites induced by Cu(II). For SMX, an ionic chemical, Cu(II) enhanced SMX adsorption significantly mainly due to Cu(II) bridging and stronger pi-pi pi interactions between SMX and Cu(II) complexes and CNTs. The complexation of SMX with Cu(II) was confirmed by the fluorescence, ultraviolet (UV), and attenuated total reflection fourier transform infrared spectroscopy (ATR-FTIR) analysis. DFT calculation further revealed that isoxazole ring nitrogen, sulfonamide nitrogen, amino nitrogen, and sulfonyl oxygen were the four possible binding sites in SMX with Cu(II). The adsorbed Cu (II) on CNTs/CoFe2O4 could form complexes with SMX, and the binding between SMX and Cu(II) enhanced the pi-pi interactions between SMX and CNTs. These two aspects led to the enhanced adsorption of SMX. This study provides new insights into the molecular interactions among Cu(II), SMX, and CNTs, and it sheds lights on the adsorption mechanisms of organic pollutants by CNTs in the presence of metal ions.