The invention relates to a modified nitrogen control material prepared from lake sediments, a preparation method and application thereof. The method includes: collecting lake sediments, conducting freeze drying, grinding and sieving for standby use; then subjecting the treated lake sediments to constant temperature heating treatment, then performing cooling, and adding zeolite into the sediments in proportion, mixing the materials evenly, then adding a mixed solution of a salt solution and an alkaline solution, carrying out oscillation impregnation modification, then conducting filtering and cooling to obtain residue, i.e. the sediment modified nitrogen control material. The method provided by the invention adopts lake sediments as the raw materials, the prepared modified nitrogen control material has significantly enhanced ammonia nitrogen adsorption performance, especially has good ammonia nitrogen removal effect on lake sediment interstitial water, the materials are cheap, the safety is high, the social and economical benefits are good, also the material has no ecological risk to lake water, is energy saving and environment-friendly, and can be applied to the lake sediment-water interface nitrogen pollution control field.