The invention belongs to the field of crops fertilizers and in particular relates to an ecological functional phosphatic fertilizer and a preparation method of the ecological functional phosphatic fertilizer. The ecological functional phosphatic fertilizer is mainly prepared from phosphatic fertilizer, organic wastes and an ecological function conditioner; the organic wastes are treated firstly, and then are subjected to conjugation reaction with the phosphatic fertilizer under the existence of an active agent to form the ecological functional phosphatic fertilizer. The ecological functional phosphatic fertilizer adopts the organic wastes as main organic matters, the organic wastes are combined with the phosphatic fertilizer to increase the moving distance of the phosphatic fertilizer in the soil, the phosphatic fertilizer is prevented from being immobilized by metal ions such as iron ion, aluminum ion and the like in the soil, the soil can be improved, the soil aggregated structure is increased, the organic matters in the soil are improved, the soil caking phenomenon is improved, the microorganism activity is improved, the stress-resistant, disease-resistant, drought-resistant and water-retaining capacity of the crops is improved, while the phosphatic fertilizer is provided, the organic wastes can be reasonably utilized, the resources can be reasonably utilized, the environment burden is reduced and the ecological functional phosphatic fertilizer is environment-friendly.