The invention belongs to the technical field of manure, and particularly relates to fermented low-value fish water-soluble manure and a preparation method thereof. The preparation method includes the steps that S1, ocean low-value fishes are chopped into chopped blocks, then water, ethylenediamine tetraacetic acid disodium and alkyl polyglucoside are added into the chopped blocks, the pH value of a system is adjusted from 3 to 5, the mixture stands and is filtered after stirring, and purified chopped blocks are obtained; S2, the chopped blocks are smashed into minced fillets which are transferred into a fermenting tank, then molasses, bacillus, lactic acid bacteria and yeast are added, the mixture is fermented at room temperature, stirring is continuously carried out during fermentation, and then fermented fish melt is prepared; S3, preservative is added into the fermented fish melt, the mixture is stirred uniformly, and the fermented low-value fish water-soluble manure is obtained. The salt content of the manure is smaller than 2%, the sum of arsenic and other heavy metal is smaller than 20 ppm, and the fermented low-value fish water-soluble manure is rich in active peptide, immunopolysaccharide, amino acid, unsaturated fatty acid and others, and can increase earth temperature after being applied into soil, improve the activity of root systems and enhance the cold resistance of crops to promote growth of the crops.