Heterogeneous catalytic systems with water as the solvent often have the disadvantage of cross-contamination, while concerns about the purification and workup of the aqueous phase after reactions are rare in the lab or industry. In this context, designing and developing the functional selective solid adsorbent and revealing the adsorption mechanism can provide a new strategy and guidelines for constructing supported heterogeneous catalysts to address these issues. Herein, we report the stable composite adsorbent (Fe/ATP@PPy: magnetic Fe3O4/attapulgite with the polypyrrole shell) that features an integrated multifunctional surface, which can effectively tune the selective adsorption processes for Cu2+, Co2+, and Ni2+ ions and nitrobenzene via the cooperative chemisorption/physisorption in an aqueous system. The adsorption experiments showed that Fe/ATP@PPy displayed significantly higher adsorption selectivity for Ni2+ than Cu2+ and Co2+ ions, especially which exhibited an approximate 100.00% removal for both Ni2+ ions and nitrobenzene in the mixture system with a low concentration. Furthermore, combined tracking adsorption of Ni2+ ions and X-ray photoelectron spectroscopy characterization confirmed that the effective adsorption occurs via ion transfer coordination; the pathway was further validated at the molecular level through theoretical modeling. In addition, the selective adsorption mechanism was proposed based on the adsorption experiment, characterization, and the corresponding density functional theory calculation.