The invention relates to a method for identifying rice nitrogen efficient varieties in a seedling stage. The method comprises the following steps: selecting a healthy and full variety to be tested, soaking seeds for 2 days at the temperature of 25-35 DEG C, accelerating germination for one day and a half at the temperature of 40 DEG C, and then seeding in cleaned sand without any nutrients and culturing until seedlings have 2 leaves and 1 heart; taking the seedlings which uniformly grow, washing with clear water and then transferring into a nitrogen-free medium; after one week of culture, transferring the seedlings into a control medium and an N-feedback medium for culturing; after that, measuring the areas LA of the rice leaves as well as the corresponding dry matter weight LDW, root weight RW and root number RN; determining a nitrogen physiological feedback value so as to determine whether the rice is the nitrogen efficient variety or not, wherein the higher the nitrogen feedback index is in the seedling stage, the higher the nitrogen utilization rate of the rice is. By establishing a specific hydroponic system and determining the nitrogen feedback index of the seedling stage bymeasuring the leaf and root indexes of the rice in the nursery stage, the method can quickly and efficiently evaluate the nitrogen efficient utilization characteristic of the rice.