Sediment capping is an in situ treatment technology that can effectively restrain nutrient and pollutant release from the sediment in lakes and reservoirs. Research on sediment capping has focused on the search for effective, non-polluting and affordable capping materials. The efficiency and mechanism of sediment capping with modified palygorskite in preventing sediment ammonia nitrogen (NH4+-N) release to surface water were investigated through a series of batch and sediment capping experiments. Purified palygorskite and different types of modified palygorskite (i.e. heated, acid-modified and NaCI-modified palygorskite) were used in this investigation. Factors affecting control efficiency, including the temperature, thickness and grain size of the capping layer, were also analysed. The batch tests showed that the adsorption of NH4+-N on modified palygorskite achieved an equilibration in the initial 45 min, and the adsorption isotherm followed the Freundlich equation. Sediment capping experiments showed that compared with non-capped condition, covering the sediment with modified palygorskite and sand both inhibited NH4+-N release to the overlying water. Given its excellent chemical stability and strong adsorption, heated palygorskite, which has a NH4+-N release inhibition ratio of 41.3%, is a more effective sediment capping material compared with sand. The controlling effectiveness of the modified palygorskite increases with thicker capping layer, lower temperature and smaller grain size of the capping material.