A method for preparing a low molecular weight fish peptide through a Bacillus natto fermentation method comprises the following steps: taking fish to mince, adding water, adding maltose, glucose, lactose or sucrose to obtain a mixture; adjusting the pH value of the mixture, sterilizing at high temperature; cooling, inoculating Bacillus natto seed liquor to ferment; and centrifuging fermentation liquor, filtering, concentrating, drying and grinding to obtain a low molecular weight fish peptide product. The method uses fish as the raw material and utilizes the Bacillus natto fermentation technology to obtain the low molecular weight fish peptide. The product in the invention is very soluble in water, is digested and absorbed easily by human body and has various functions of reducing cholesterol in the blood, promoting lipid metabolism, preventing and curing hypertension and the like. The technology in the invention is also suitable for other low value aquatic product and high-grade aquatic product machine leftover pieces, thus fish resources can be fully utilized; and the technology is simple and easy, the investment is less, the cost is low, the effect can be realized fast, the added value is high and the method is suitable for large-scale industrial production.