The invention provides an anti-counterfeiting method using DNA specific complementation, and belongs to the field of anti-counterfeiting technologies. The method comprises the following steps: synthesizing a gene sequence at random and then synthesizing a complementary gene sequence of the gene sequence, connecting the complementary gene sequence to a carboxyl group and mixing with an Fe3O4 solution containing a surface-modified amino group and reacting to obtain a probe solution; preparing a gene sequence solution from the gene sequence, placing the gene sequence solution onto a vector, standing and drying to obtain a dried vector, and placing the dried vector onto a sample to be tested; placing the probe solution at the position where the gene sequence solution is on the vector during detection, hybridizing and washing; attaching a magnetic sticker to the washed vector, and detecting that the sample to be tested is genuine if the magnetic sticker is not separated from the washed vector after attached to the washed vector. The anti-counterfeiting method can realize the anti-counterfeiting identification specifically, efficiently and sensitively.