<p>Achieving rapid and accurate detection of foodborne viruses from complex clinical samples, especially stool samples, has long been a challenge in on-site testing. We report a fluorescent lateral flow immunoassay (LFA) based on ultra-stable magnetic fluorescent tag (FeDQD@Si) with a protected SiO₂ shell, enabling simultaneous and quantitative detection of two key foodborne viruses, including norovirus (NoV) and adenovirus (AdV). The FeDQD@Si tag enables efficient capture of target viruses from complex samples and achieving ultrahigh sensitivity on LFA strips at pg/mL levels via magnetic enrichment and fluorescence signal amplification from multi-QDs fluorescence superposition. The SiO₂ shell not only protects the luminescence performance of magnetic fluorescent tags in stool samples but also enhances flowability during the chromatography process and suppresses background signals from complex samples. The established FeDQD@Si-LFA for NoV and AdV achieved detection limits of 0.725 pg/mL and 1.28 pg/mL, respectively, about two orders of magnitude lower than traditional AuNP-based LFA. In testing 75 clinical stool samples, the sensitivity of FeDQD@Si-LFA relative to the gold-standard qPCR reached &gt; 92%, with a specificity of 100%. Collectively, this platform holds great potential for on-site detection of foodborne outbreaks and rapid clinical diagnosis of gastrointestinal infections.</p> Graphical abstract <p></p>