The invention belongs to the technical field of chemical synthesis, and specifically relates to a preparation method of a polyurethane elastomer composition for sustained release of fertilizer. The composition is prepared from a polymer component and a prepolymer component. The preparation method is scientific, reasonable, easy and practicable. The prepared composition is coated on the surface of fertilizer, so the releasing speed of fertilizer nutrients is slow, the releasing period is long, and the released fertilizer can satisfy the nutrient need of crops during the whole growth period.