The invention relates to the technical field of agricultural compound fertilizers and in particular relates to an ecological compound fertilizer capable of enhancing disease resistance and a preparation method thereof. The ecological compound fertilizer contains the following components in parts by weight: 50-60 parts of compound fertilizers, 30-50 parts of organic wastes, 45-55 parts of carboxymethyl starch, 15-18 parts of medical stone, 8-12 parts of kaolin, 8-15 parts of diatom ooze, 3-7 parts of humic acid, 10-15 parts of microbial strains, 3-6 parts of polyglutamic acid and 5-10 parts ofsodium lignin sulfonate. The ecological compound fertilizer prepared according to the invention has a certain slow release performance and effects of activating the biological activity, promoting rootgrowth of crops, accelerating decomposition of organic matters, providing rich nutrition, enhancing the disease resistance of crops and the like. The absorption of the crops on nutrient elements is promoted, the micro-ecological environment of soil is effectively improved, the microbial population in the soil is improved, the absorption of the crops on the nutrient elements is promoted, the quality of the crops is improved, stress resistance of the crops is enhanced, and soil fertility is improved.