Background Natural zeolite, abundant hierarchically porous structure aluminosilicate mineral, have high affinity to ammonium in solution. A considerable amount of literature has been published on the removal of ammonium in waters by zeolite, but mainly focused on the low-content and even trace ammonium. Few literatures were reported about the natural zeolite as adsorbent to remove high-level of ammonium in coal chemical wastewater. Therefore, adsorption mechanism of high-concentration ammonium in aqueous solution using Chinese natural zeolite was disclosed by the strategy of experimental optimization combining with Molecular Dynamics simulation. ResultsThe natural zeolite presented unique adsorption performances for high- ammonium distinguish from that of low ammonium, which were characterized as exhibiting faster adsorption rate, greater loading capacity and apparent desorption. The hybrid physical-chemical adsorption as the mechanism was induced from the adsorption kinetics and isotherm study in 4000 mg-N/L solution. Besides to the electrostatic attraction between the framework and guest ammonium exchanged by metal cations in the zeolite framework, the existence of the chemical bonding and hydrogen bonding forces was supported experimentally from the ion exchange capacity (IEC) investigation by the great disequilibrium between the total exchanged metal cations and ammonium. Moreover, the above were confirmed theoretically by the calculated results in the perspective of bonding strength in MD simulation. Considering comprehensively, we concluded physisorption dominated the initial adsorption stage as multilayer adsorption and chemisorption governed the subsequent adsorption process as monolayer form. Besides, the putative explanation for the desorption-occurrence was given that most ammonium concentrated in the channel openings physically, and transferred into the bulk solution preferentially through the mesopores and macropores. Conclusions Overall, we have demonstrated that the Chinese natural zeolite had the potential to capture high-concentration ammonium in wastewater remediation effectively. Considering with several research thinking comprehensively, this investigation enriched the adsorption mechanism research, and provided a novel insight for designing a workable approach for rapidly alleviating subsequent water decontamination processes using low-cost abundant minerals.