The invention discloses a preparation method of a seedling culture medium of watermelon seedlings. The preparation method comprises the following steps: (1) uniformly mixing straws, rice husks, sawdust, biogas residues, mushroom residues and wine residues to obtain a fermentation medium; (2) adding a fermentation bacterial agent into the fermentation medium, and laminating, composting and fermenting to obtain a composted fermentation product, wherein the fermentation bacterial agent is mixed bacteria of saccharomycetes, actinomycetes, lactobacillus and bacillus subtilis; the saccharomycetes is pichia pastoris, the actinomycetes is streptomyces albus, the lactobacillus is lactobacillus acidophilus and the bacillus subtilis is bacillus vallismortis; (3) mixing the composted fermentation product with pearlite to obtain the seedling culture medium of the watermelon seedlings. The preparation method of the seedling culture medium of the watermelon seedlings has the advantages that the preparation method is simple, the cost is low, the cultured watermelon seedlings are stronger, the quality of the watermelon seedlings is good, the total dry weight of the watermelon seedlings is remarkably improved, the root density is remarkably improved and the like.