In this study, surfactant modified zeolite-clinoptilolite (SMZ) by CPB (cetylpyridinium bromide) was used for simultaneous removal of ammonium, nitrate and phosphate in synthetic wastewater, and the sorption properties of SMZ were determined and compared with natural zeolite. Results showed that natural clinoptilolite had good affinity for ammonium (8.940 mg/g), but not for nitrate (0.427 mg/g) and phosphate (0.801 mg/g). With the increase of surfactant loading from 5 g/L to 40 g/L, the sorption capacity for nitrate increased from 0.462 mg/g to 4.661 mg/g. when the surfactant loading is 40 g/L, the SMZ has a phosphate adsorption capacity of 2.119 mg/g. The SMZ had a significant enhancement on nitrate and phosphate sorption, could simultaneously remove ammonium, nitrate and phosphate at specific conditions, with removal efficiency up to 85.2%, 83.1% and 56.7%, respectively. Orthogonal experiments showed that ammonium concentration was the most important factor for ammonium sorption on SMZ. Surfactant loading was the major factor for nitrate and phosphate sorption. With the increase of surfactant loading from 5 g/L to 40 g/L, the sorption capacity for nitrate increased from 0.462 mg/g to 4.661 mg/g. When the surfactant loading is 40 g/L, the SMZ has the best phosphate adsorption capacity 2.119 mg/g. Samples were characterized by X-ray diffraction (XRD) and Brunauer–Emmett–Teller (BET). Semi-empirical quantum mechanics molecular simulation indicated that electrostatic attraction existed between CPB and dihydrogen phosphate ion. Results indicate that SMZs might have great potential of removing cations and anions simultaneously in the aquatic environment, which is good for eutrophication control and nutrients removal.