A layered fertilization cultivation method of annual agricultural economic crops comprises steps of soil loosening, disinfection, soil preparation, bait throwing, clay fertilizer application, chemical fertilizer application, organic fertilizer application, soil covering and seedling planting, root protection, watering and the like so as to enable a cultivation base to form a substrate layer (1), a clay fertilizer layer (2), a chemical fertilizer layer (3), an organic fertilizer layer (4), a seedling separation soil layer (5) and a seedling protection soil layer (6) from bottom to top and accordingly the layered fertilization cultivation is achieved. Compared with the existing method that the fertilization is performed after cultivation and green returning of seedlings, the labor is saved, the cultivation is convenient, and the damage to the seedlings when the fertilization is performed later can be avoided; the fertilizer protection is facilitated and the nutrient loss caused by the scattering of the fertilizer due to the rain is avoided; the concentrated supply of the fertilizer is facilitated and the crop growth is facilitated; the fertilization is performed first, then the seedlings are planted, namely that the fertilizer waits for the seedlings, and accordingly fertilizer nutrients can be timely obtained when the seedlings survive and return to green; the growth speed can be improved due to the comprehensive effect of the layered fertilization cultivation method, the healthy growth of the seedlings is achieved, and the harvest is increased.