Many serious public health emergencies around the globe are caused by viral epidemics. Thus, developing a reliable method for viral screening is in high demand. Multiplex assays for simultaneous detection and fast screening of high-risk pathogens are especially needed. This study employs metal nanoparticles to generate specific mass spectral signals for different RNA viruses, which enables simultaneous detection of whole viruses by laser desorption/ionization mass spectrometry (LDI-MS). We developed a nanoparticle-based sandwich immunosorbent assay as a sensing platform for the detection of viruses and viral nonstructural protein by LDI-MS. Cellulose acetate membrane (CAM) serves as the substrate for the fabrication of the sandwich immunosorbent assay with the advantages of clean mass spectra and high enrichment of analytes. Antibody-modified metal nanoparticles (Ab− MNPs; M = Au or Ag) act as metallic biocodes for the LDI-MS detection. The signal amplification readout for the virus is through the pulsed laser-induced formation of metal cluster ions ([M n ] + ; n = 1−3) from the Ab−MNPs which specifically bind on the CAM. Our sensing system is effective for the detection of intact viruses [Enterovirus 71 (EV71) and Japanese encephalitis virus (JEV)], nonstructural protein 1 (NS1) of Zika virus (ZIKV), EV71-spiked human serum samples, and the simultaneous detection of EV71 and ZIKV. Our probe efficiently detects EV71 in real clinical serum samples with >95% agreement with RT-qPCR results. This high-throughput LDI-MS viral detection system is simple, reliable, and high-throughput. We believe this platform has the potential to be employed for the routine screening of patients with viral infections.