The invention relates to the field of foods, and discloses a preparation method of canned sauries low in histamine. The preparation method comprises the following steps of performing unfreezing, performing histamine removing treatment, performing dicing and cleaning, performing canning and cooking, preparing materials, performing exhausting, and performing sealing and sterilization. In the steps of performing histamine removing treatment and performing dicing and cleaning, the sauries are treated with a histamine treating agent, and the histamine treating agent is a bacteria-free water solution containing shell calcined powder, lecithin, soluble chitosan and lysozymes. The histamine treating agent not only can adsorb and remove the histamine, but also can kill microorganisms generating thehistamine, restrains bioactivity of the microorganisms generating the histamine, and is notable in effect of reducing the content of histamine. The raw materials are easy to obtain, the preparation method is simple, organic solvents are not used, a penetrant and a dispersing agent do not need to be added additionally, the content of the histamine is reduced, and besides, the content of calcium inproducts can also be increased. The nutrient components of the products are enriched, and the histamine treating agent can be used as a fresh keeping agent. The preparation technology is simple, thecost is low, and the preparation technology is suitable for industrialized production.