Shigella, a typical and fatal foodborne pathogen with strong infectivity and survivability in foodstuff, demands a simple and sensitive detecting method. In this study, we reported a novel nanoplatform based on biofunctionalized magnetic nanoparticles (MNPs) modified upconversion nanoparticles (UCNPs) for rapid and specific determination of Shigella. Due to base pairing, Shigella aptamer-functionalized horseradish peroxidase (HRP) combined with complementary strand-modified MNPs@UCNPs. In the absence of Shigella, HRP associated with MNPs@UCNPs were magnetically separated, and colorless 3,3′,5,5′-tetramethylbenzidine (TMB) was oxidized into blue oxTMB. The overlap between oxTMB’s absorption peak and MNPs@UCNPs’ emission peak caused the fluorescence quenching at 545 nm. The MNPs@UCNPs fluorescence biosensor was achieved to detect Shigella in 1 h, with a limit of detection of 32 CFU/mL. This work showed a rapid and specific sensing platform and produced satisfactory chicken sample results.