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The invention relates to a high-energy composite peptide selenoprotein nutrient solution, a preparation method and an application thereof. The nutrient solution is composed of selenium raw material, protein, mineral substances, vitamin, natural energy minerals and the like; the high-energy composite peptide selenoprotein nutrient solution containing rich selenium element, the mineral substances, the vitamin and natural energy substances is prepared by performing enzymolysis on the protein, and conducting synthesizing, energy treatment, complexation and strengthening treatment on a peptide selenoprotein compound, and the nutrient solution can be widely used for the development and utilization of various selenium-enriched agricultural and sideline products (comprising various food crops, vegetables, fruits, fungi, wild plants, marine food, animal meat and Chinese medicinal herbs). The application of the nutrient solution is as follows: the high-energy composite peptide selenoprotein nutrient solution mother solution is diluted by 6000-8000 times in multiple proportions by adding water, the diluted nutrient solution is irrigated and sprayed to the roots and leaf surfaces of the crops in different growth periods for 3-6 times, and therefore, the selenium-enriched agricultural and sideline products can be obtained.