The invention provides a polypeptide chelated potassium zinc urea fertilizer and a preparation method thereof, and belongs to the technical field of fertilizer. The fertilizer uses poly-aspartic acid as a chelating agent, and adds 5 kg of polypeptide chelated potassium zinc stock solution into each ton of urea based on the traditional urea. The fertilizer is a novel high efficiency nitrogenous fertilizer, can supply nitrogen, potassium, zinc elements required by plant, can improve the rate of absorbtion and utilization of the plant for the nutrient elements in soil, can supply biological growth elements evenly, and has strong synergistic effect for the nitrogenous fertilizer, potash fertilizer, and phosphate fertilizer. The chelating agent can be biodegraded, and has no pollution for the plant and the soil. The polypeptide chelated potassium zinc stock solution and urea solution can pass two-stage conveying devices of urea solution pump and fusion pump in the preparation method, so that the mixture can be mixed uniformly, and the stability of the product quality can be guaranteed. The polypeptide chelated potassium zinc stock solution is added into the inlet of the urea solution pump, and the moisture of the product can be controlled effectively after performing primary evaporation, granulation and cooling.