The invention discloses a special organic fertilizer for rice in the booting stage, and a preparation method of the fertilizer, and relates to the field of organic fertilizers. The special organic fertilizer is prepared from, by weight, 45-55 parts of straws, 8-10 parts of soybean meal, 6-8 parts of cottonseed meal, 3-5 parts of mushroom residues, 4-6 parts of lignin residues, 1-2 parts of wheat bran, 8-10 parts of rice chaff, 3-5 parts of fish meal, 2-4 parts of licorice root powder, 1-3 parts of a mineral additive, 0.5-1 part of trace elements and 5-10 parts of amino acids. The organic fertilizer contains a large amount of organic matters, shows the soil granule structure improving, activating, loosening and changing properties and the physical and chemical properties of organic fertilizers, and increases the water storage and fertilizer conservation ability of soil; and the organic fertilizer provides various trace mineral matter elements needed by the booting stage, has the fast action property of chemical fertilizers, can prevent and treat various physiologic diseases caused by missing trace elements in the booting stage in order to reduce other diseases and make the rice vigorously grow in the whole booting stage, and lays a good foundation for final fruiting.