The invention relates to the technical field of seedling matrixes of crops and particularly relates to a rice seedling matrix and a preparation method thereof. The rice seedling matrix with good permeability and high fertility is particularly prepared from the main raw materials of crop straws, cow mature, rice husk, seed cakes, microbial zymophyte and the like through steps of material preparation, soaking, straw piling, straw composting, matrix preparation and the like. The rice seedling matrix comprises the following main raw materials in percentage by weight: 35%-45% of the crop straws, 27%-34% of the rice husk, 16%-24% of the cow mature and 7%-15% of seed cakes, wherein 1kg of the microbial zymophyte is used in each 5-6 cubic meters of the crop straws. According to the preparation method, the soil-free matrix production is realized, the utilization of non-renewable resources is reduced, the damage caused to farmland soil resources is reduced, the environment is protected, the factory seedling is realized, the cost is lowered, the plant diseases and the insect pests are reduced, the content of soil organic matters is increased, and the yield and the milled rice rate can be increased.