The invention discloses a self-permeating type soil heavy metal repair agent and a preparation method thereof, and belongs to the technical field of repair agent preparation. According to the self-permeating type soil heavy metal repair agent and the preparation method thereof, organic matter is mixed with a base material of organic acid, the promoting property of the repair agent on growth and development of plants is effectively improved, physical properties of repaired soil are improved, activities of microorganisms and soil organisms are promoted, nutrient elements in the soil are promotedto be decomposed, and meanwhile, air permeability, permeability and adsorbability of the soil are changed; by addition of mineral improvers such as zeolite, peat, charcoal, weathered coal and the like, on one hand, reaction performance such as adsorption, ion exchange and the like of heavy metal elements is improved, heavy metal pollutants such as cadmium, chromium, lead and the like in soil canbe cured and passivated, bio-availability of the heavy metal pollutants and mobility in soil are reduced, risks that the pollutants are absorbed by crops and transferred to food chains are reduced, and on the other hand, physical and chemical properties of the soil are improved.