The invention relates to a preparation method of an organic selenium fertilizer. The fertilizer at least comprises the following materials: fulvic acid, sodium selenite, chicken manure, and crop straw. The organic fertilizer whose selenium content reaches to 12-15ppm employs natural biological materials, and contains organic nitrogen, phosphorus and potassium which provide high-quality nutrition for plants and crops; the organic fertilizer has the advantages of multiple and long-acting functions, production and income increasing, quality improvement, disease resistance, drought tolerance, water retention, soil conservation, and environmental protection; the organic fertilizer provides powerful protection for people to produce green foods. The production process is simple, equipment investment is low, and the method is easy to promote industrially.