Rapid and early diagnosis of respiratory viruses is key to preventing infections from spreading and guiding treatments. Here, we developed a sensitive and quantitative surface-enhanced Raman scattering-based lateral flow immunoassay (SERS-based LFIA) strip for simultaneous detection of influenza A H1N1 virus and human adenovirus (HAdV) by using FeO@Ag nanoparticles as magnetic SERS nanotags. The new type of FeO@Ag magnetic tags, which were conjugated with dual-layer Raman dye molecules and target virus-capture antibodies, performs the following functions: specific recognition and magnetic enrichment of target viruses in the solution and SERS detection of the viruses on the strip. Based on this strategy, the magnetic SERS strip can directly be used for real biological samples without any sample pretreatment steps. The limits of detection for H1N1 and HAdV were 50 and 10 pfu/mL, respectively, which were 2000 times more sensitive than those from the standard colloidal gold strip method. Moreover, the proposed strip is easy to operate, rapid, stable, and can achieve high throughput and is thus a potential tool for early detection of virus infection.