The invention discloses a selenium-enriched ecological bacterial fertilizer and a preparation method thereof, and belongs to the technical field of preparation of fertilizers. The selenium-enriched ecological bacterial fertilizer comprises the following raw materials: urea, urea phosphate, diammonium phosphate, potassium nitrate, boric acid, selenium potassium phosphate, zinc sulfate, corn straws,a biogas slurry, an EM bacterial liquid, a straw fermentation inoculant, CM bacteria, soybean lecithin, lignin, sodium alginate, chitin, an EM bacterial liquid, mushroom residues, selenium humate, aselenite, brown sugar, selenohomocystine, beta-oligomeric acid, stearic acid, sodium hexametaphosphate, N,N-dimethylformamide, ammonium persulfate, selenium ore powder, itaconic acid, dibutylcarboxyltoluene, silane coupling agent KH-550, diethylenetriamine, attapulgite, o-phenyl benzoic acid and polyvinyl alcohol. The selenium-enriched ecological bacterial fertilizer provided by the invention isprepared by the steps of preparation of compound fertilizer particles, preparation of a film coating material liquid, coating of the fertilizer particles and drying; and the ecological bacterial fertilizer provided by the invention can improve the yield of crops and the content of a selenium element.