Heavy metal ion pollution poses significant risks to human health and ecological systems, and its monitoring is important. A sensitive and accurate surface-enhanced Raman spectroscopy (SERS) detection assay for Hg2+ was developed using Au@Ag/COF substrates and Y-shaped DNA labeled with two Raman reporters. The Au@Ag NPs in the COF produced robust and uniform E-fields, improving their detection reproducibility. The Y-shaped DNA design increased sensitivity with a low detection limit of 5.0 × 10−16 M by bringing the Raman reporter closer to the substrate surface. Additionally, the use of two Raman reporters allowed for a ratiometric method, improving detection accuracy by detecting both “signal-off” and “signal-on” signals. This selective sensor exhibited excellent recovery in river water, tap water, and milk samples, showcasing its robust biosensing capability for the detection of Hg2+ and its potential for sensing other heavy-metal ions in food and environmental applications.