The invention relates to a heavy metal mercury ion detection method based on nucleic acid aptamer labeling and belongs to the field of environmental analysis. A Fe3O4/Au magnetic material of a core-shell structure is prepared, nucleic acid aptamer medication is conducted on the surface of a substrate, and enrichment and separation of mercury ions in an actual water sample are achieved by utilizing the T-Hg-T effect between Hg ions and a nucleic acid aptamer and the magnetism of the substrate. A series of experiments prove that a preparation method and an analysis method adopted by the invention are simple and convenient to operate, and selective detection of mercury ions can be achieved.