The invention relates to a method for preparing an anti-counterfeiting modal fiber, including: mixing a pulp stock solution with a cellulose catalyst, alkalizing, aging, sulfonating, and then dissolving the pulp stock solution in an alkaline solution to obtain a treatment solution; mixing the treatment solution with multiple amino acid-metal chelates, filtering, defoaming and ripening to obtain a spinning stock solution; and mixing the spinning stock solution with a spinning bath additive, and wet spinning, followed by drafting, defoaming, desulfurizing, water washing, and other post-treatments, to obtain an anti-counterfeiting modal fiber, wherein the amino acid metal-chelates account for 0.5%-1.5% by weight of the spinning stock solution. Amino acid-metal chelates are used to anti-counterfeit and encrypt the modal fibers, and the anti-counterfeiting and encrypting is involved in the spinning stock solution of modal fibers. The fiber source can be tracked and identified by detecting the species of metal elements and amino acids.