The invention discloses a special medicinal rhubarb organic fertilizer and a manufacturing method thereof, and belongs to the technical field of fertilizers. The organic fertilizer is prepared from, by weight, 30-40 parts of cow dung, 5-10 parts of bamboo charcoal, 2-5 parts of fulvic acid, 1-3 parts of nicotinic acid amide, 20-30 parts of chicken manure, 10-15 parts of chimney ash, 1-5 parts of attapulgite powder, 20-30 parts of bran, 20-25 parts of fish bone meal, 20-30 parts of salt, 10-15 parts of sodium carbonate, 20-25 parts of guano, 15-20 parts of sunflower straw ash, 5-7 parts of medical stone powder, 5-10 parts of carnallite, 3-7 parts of polyterpene bacillus agents, 5-8 parts of actinomycete agents, 5-7 parts of glauconite, 10-15 parts of seaweed, 5-10 parts of fatty acid, 3-10parts of dolomite, 1-3 parts of zeolite, 2-5 parts of oxalic acid and 5-8 parts of potassium salt. According to the organic fertilizer, stress resistance of medicinal rhubarb can be effectively improved, reproduction of harmful and pathogenic microorganisms in soil can be effectively restrained, the acre yield of the medicinal rhubarb can reach 742kg or more after the organic fertilizer is applied, and the incidence rate of root rot diseases of the medicinal rhubarb is lower than 27%.