<p>The extensive use of ammonium sulfate as a leaching agent in the mining process of ion-adsorption rare earth ores (IAREO) has led to severe pollution of ammonia nitrogen in the wastewater of historical residual ores. In this study, natural clinoptilolite was modified using sodium hexametaphosphate (SHMP) to elucidate both the enhanced adsorption performance and the fundamental mechanisms governing NH₄⁺ removal. Single-factor experiments identified the optimal modification conditions as an SHMP concentration of 0.1&#xa0;mol·L⁻¹, a temperature of 80&#xa0;°C, and a duration of 3&#xa0;h, under which the NH₄⁺ adsorption capacity of modified clinoptilolite increased to 2.6 times that of the natural clinoptilolite. Characterization using SEM, BET, XRD, and FTIR revealed that SHMP treatment increased surface roughness and enhanced pore structure without altering the crystalline framework. Adsorption experiments demonstrated that NH₄⁺ adsorption onto the modified material conformed to the pseudo-second-order kinetic model and the Langmuir isotherm, yielding a maximum adsorption capacity of 16.72&#xa0;mg·g⁻¹, indicating a chemisorption-dominated process characterized by spontaneous, exothermic monolayer adsorption<b>.</b> Ion exchange was proven as the primary mechanism, with NH₄⁺ replacing Na⁺ in the clinoptilolite structure, while coexisting cations such as K⁺ and Ca²⁺ markedly inhibited adsorption. Additionally, the modified clinoptilolite exhibited substantial removal efficiency when applied to actual wastewater from IAREO operations. Overall, the findings demonstrate the effectiveness of SHMP-modified clinoptilolite and provide guidance for ammonia–nitrogen remediation in IAREO sites.</p>