The invention relates to a multifunctional synergistic nitrogen fertilizer and a preparation method thereof, and is applied in the field of agriculture and forestry production. The product comprises medium trace elements, a plant nutrition conditioner and a nitrogen fertilizer synergist. The product is rich in the medium trace elements, such as calcium, magnesium, sulfur, boron, manganese, zinc and the like, required by crop growth and guarantees full absorption of crop nutrition. The plant nutrition conditioner and the nitrogen fertilizer synergist can effectively promote plants to absorb nutrient elements and improve the utilization ratio of the nitrogen fertilizer. The multifunctional synergistic nitrogen fertilizer is prepared by the following steps: mixing urea, ammonium sulfate, ammonium chloride, bentonite, zinc sulfate, manganese sulfate, calcium chloride, magnesium sulfate, disodium octoborate tetrahydrate and the like according to a certain scientific ratio; adding a certain dose of plant nutrition conditioner and the nitrogen fertilizer synergist; mixing completely; and pelletizing. The multifunctional synergistic nitrogen fertilizer can prolong the useful life of the nitrogen fertilizer by 90 to 120 days, increases the utilization ratio of the nitrogen fertilizer by over 30 percent, increases yield by 15 to 20 percent, and enhances resistance, such as drought resistance, cold resistance, disease resistance and the like, of crops.