The invention relates to a method for preparing fish scale collagen. The method comprises the following steps: fresh fish scales are taken as a material, undergo cleaning, drying and crushing, are soaked in NaOH solution for degreasing, and soaked in hydrochloric acid solution for deashing; the fresh fish scale is added with water of which the weight is 5 to 10 times of that of the fish scales, the pH value is adjusted to between 2 and 4 by acid solution, pepsin of which the weight accounting for the weight of the mixing solution is between 1 and 5 percent is added, the mixing solution undergoes enzymolysis at a low temperature for 4 to 10 hours, and enzyme is killed; enzymatic liquid is filtered twice to obtain extracting solutions, the extracting solutions are mixed, the mixing solution is decolored, sodium chloride of which the weight accounting for the weight of the mixing solution is between 5 and 15 percent is added into the mixing solution for overnight salting out, deposit is separated and collected, and acetic acid of which the weight accounting for the weight of the mixing solution is between 5 and 20 percent is added into the deposit for dissolution to obtain protein solution; the protein solution is dialyzed and desalted to obtain purified collagen liquid; and the collagen liquid is subjected to freeze-drying or spray-drying and micro-crushing to obtain solid particle. The method has the advantages of reasonable process, simple operation, safety, low cost, little loss of nutrient matters of the product, low ash content and high yield and purity of the collagen.