Immunochromatographic assay (ICA) has been widely used in various fields for its economy, simplicity, sensitivity and specificity. The application of colloidal gold nanoparticles in ICA has limitations in quantification and interference resistance. Fluorescent nanomaterials have become an important signal label in ICA due to their excellent optical properties. This article briefly describes the preparation and properties of fluorescent nanolabels, such as quantum dots, up-conversion nanoparticles, time-resolved fluorescent microspheres, and persistent luminescence nanoparticles. The focus of this review is the application of fluorescence immunochromatography in the detection and analysis of foodborne pathogens, mycotoxins, pesticides, veterinary drugs, antibiotics, hormones, endocrine disruptors, heavy metals and other food hazards. The combined use of fluorescence immunochromatography with smartphones is also discussed. It is hoped that this review can provide a reference for food safety detection and on-site and real-time monitoring.