The invention relates to an organic ecological matrix for soilless culture and a preparation method thereof and belongs to the technical field of soilless culture. The organic ecological matrix for soilless culture, provided by the invention, comprises the following materials: 35-50% of rotten abandoned padding of a fermentation bed, 10-15% of rotten straws, 15-35% of rotten vinegar residues and 15-20% of medical stone, wherein the water content is 25-45%, the organic content in dry ingredients is more than or equal to 30%, the total nutrient content (N+P2O5+K2O) is 2.5-5%, the total porosity is 65-80%, the matrix volume weight is 0.48-0.63g.cm<3>, EC is 1.26-2mS.cm<1> and pH is 5.85-7.5. The organic ecological matrix is suitable for being used as the matrix for soilless culture of solanaceous vegetables. After the organic ecological matrix provided by the invention is applied to the solanaceous vegetables, the plant height, stem diameter, leaf area index, blade chlorophyll content, root activity, yield and fruit quality are obviously increased. For example, after the organic ecological matrix is applied to tomatoes, the plant height, stem diameter, blade chlorophyll content, root activity, yield and fruit quality of the tomatoes are all obviously increased, especially, the Vc content and sugar-acid ratio of the tomatoes are obviously increased.