The invention discloses a method for reducing a nitrogen fertilizer in a wheat-corn rotation system, belonging to the technical field of management of soil nitrogen nutrients. The method comprises the following steps: carrying out seed dressing on a Mn-Zn micronutrient fertilizer; adding a nitrification inhibitor and a coated controlled release nitrogen fertilizer when the nitrogen fertilizer is applied, and carrying out foliar topdressing of a boron fertilizer. By adopting the method, once fertilization of the nitrogen fertilizer in a wheat-corn planting system is achieved, the labor force is saved, materials are easily available, the operation process is simple, the fertilization method is simple and convenient, the cost is low, popularization is facilitated, and the application prospect is good. The application rate of the nitrogen fertilizer is obviously reduced, compared with the traditional fertilization in wheat and corn planting, the method has the advantage that the dosage of the nitrogen fertilizer is reduced by over 20%, loss of the nitrogen nutrients is obviously reduced, the pollution to water and an atmospheric environment is relieved, the environment risk is reduced, and the needs of agricultural sustainable development are satisfied.