Provided is a preparation method of a watermelon organic fertilizer. The fertilizer is prepared from, by weight, animal manure, wheat straw, bean pulp, traditional Chinese medicines, trace elements, urea, a phosphate fertilizer, a potash fertilizer and humic acid, wherein the traditional Chinese medicines comprise honeysuckle flowers, folium isatidis, Japanese thistle herb, sun euphorbia herb and licorice roots; the preparation method comprises the steps that the traditional Chinese medicines and the organic fertilizer are subjected to fermentation, a traditional Chinese medicine fermented concentrated solution is poured into the organic fertilizer, stirring and mixing are conducted to be uniform, and low-temperature drying is conducted; the nutrient content is detected, according to the content detection result, the urea, the phosphate fertilizer, the potash fertilizer and the trace elements are added for mixing, and the mixture is sent into a granule shaping machine for shaping; humic acid is blended according to the proportion and then added into the granules for coating; the coated granules are sent into an air flow medium-temperature dryer for drying, and the watermelon organic fertilizer is obtained. According to the preparation method of the watermelon organic fertilizer, a soil structure can be improved, the soil fertility is increased, the watermelon yield is increased, and the watermelon quality is improved. Meanwhile, harmful microorganisms are inhibited to survive and reproduce, soil-borne diseases and insect pests and continuous cropping obstacles are relieved and gradually eliminated, water seepage, water retention and air permeable capacities are enhanced, soil granulation is promoted, the viable content is high, and the fertilizer is green and free of residue.