The present invention relates to the field of food and discloses a preparation method of low histamine scombrida fish fillets. The preparation method comprises the following steps: pretreating, thawing, washing, slicing, secondary washing and freezing. In the washing and secondary washing steps, the fish fillets are treated with a histamine treatment agent. The histamine treatment agent is a sterile aqueous solution of shell calcined powder, zeolite powder, lecithin, soluble chitosan and lysozyme. The histamine treatment agent can absorb and remove histamine, can also kill microorganisms producing the histamine, inhibits biological activities of the microorganisms producing the histamine, significantly reduces a histamine content, at the same time can remove heavy metals in fish meat, is easy to get raw materials and simple in the preparation method, does not use organic solvents, is free of extra additions of penetrants and dispersants, reduces the histamine content, at the same timealso increases a calcium content of products, enriches a nutritional content of the products, and can also be used as a preservative for use. The preparation method is simple in technology, low in costs and suitable for an industrialized production.