<p>Effective epidemic control hinges on rapid point-of-care detection of respiratory viruses, but the sensitivity of current screening technologies remains inadequate. Here, we developed a CRISPR-activated, colorimetric Surface-Enhanced Raman Scattering (SERS) dual-mode nucleic acid lateral flow assay (LFA) that enables highly sensitive, flexible, and simultaneous detection of two common respiratory viruses, influenza A (H1N1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). By coupling recombinase polymerase amplification with CRISPR for sensitive amplification and specific target recognition, viral targets activate Cas13 trans-cleavage to efficiently cleave reporter probes. In parallel, a dual-functional magnetic SERS tag (Fe₃O₄@Au/Au-SA) was introduced, which captures two biotinylated reporter molecules through streptavidin modification, and generates strong and stable SERS signals through built-in hotspot effects. The resulting CRISPR-magnetic SERS-LFA enables rapid qualitative screening of H1N1 and SARS-CoV-2 through reduced colorimetric signal intensity on two test lines and accurate quantification via SERS signal changes. The establish method achieves a detection limit of 7–9 copies/µL for the two target viruses and shows good agreement with quantitative reverse transcription polymerase chain reaction (qRT-PCR) in validation with 74 clinical samples. Both the sensitivity and specificity for clinical samples reach 100%, highlighting its potential for field deployment.</p> Graphical Abstract <p></p>