The invention relates to a preparation method of a compound ecological fertilizer from plant stalks. The compound fertilizer is prepared by degrading a main raw material of plant stalks under the action of small molecule organic acid in the presence of a solid super acid catalyst, and combining with distiller's grains, bone meal, bran leather, humic acid, and NPK fertilizer. The raw materials consist of, by weight, 60-80 parts of plant stalks, 5-10 parts of distiller's grains, 5-15 parts of bone meal, 5-15 parts of wheat bran, 5-10 parts of humic acid and 30-50 parts of NPK fertilizer. The method uses a catalytic degradation technology for preparation of the compound ecological fertilizer, reaches high catalytic degradation efficiency of stalks, completes the conversion from stalks to compound ecological fertilizer within 16h at the highest speed, and has the advantages of simple operation, low cost, recyclable catalyst, and no corrosion of equipment, and can quickly obtain the product. The prepared compound ecological fertilizer can effectively enhance fertilizer efficiency, stimulate crop growth, control pests and diseases, improve the quality of agricultural products, and the absorb soil pollutants, improve the water retention capacity of soil and fertilizer and improve soil structure, and is conducive to the sustainable development of agriculture.