In this study, magnetic zeolite (MZ) nanocomposite modified with cysteine was developed in order to enhance selectivity and capacity of clinoptilolite for cadmium ion. The prepared MZ nanocomposite is containing clinoptilolite and magnetite nanoparticles with weight ratio of 3:1. The synthesized nanocomposite was characterized by transmission electron microscopy, X-ray diffraction and vibrating sample magnetometer. Surface modification was confirmed by Fourier transform infrared spectrometer. Experiments were carried out to find the optimum conditions for modification of clinoptilolite and to investigate the effective parameters (pH, adsorbent dosage, contact time, and temperature) on the adsorption of Cd2+ ion by modified clinoptilolite. The results showed enhanced selectivity of modified MZ in the presence of other naturally occurring cations (Na+, K+, Ca2+ and Mg2+) and ammonium. Kinetic and equilibrium data were well fitted by a pseudo second-order and Langmuir model, respectively, with high correlation coefficients. The maximum adsorption capacities of the modified and non-modified clinoptilolite were found to be 20.0 mg/g and 5.2 mg/g, respectively. Thermodynamic parameters revealed that the adsorption process is spontaneous and endothermic under studied conditions.