Microcystins (MCs) is toxic substances that may affect the safety and quality of seafood and aquatic products through water contamination, thus posing a potential threat to both human health and the ecosystem. When MCs exists in water, it can lead to contamination of aquatic plants and animals, which can affect other organisms in the food chain. Therefore, monitoring and controlling the level of MCs in water can ensure that seafood and aquatic products do not contain harmful substances, thereby safeguarding the health and safety of consumers. It also ensures that the quality of aquatic products meets hygiene standards and improves the market competitiveness of the products. This article reviews the application of different fluorescence nanomaterials in the assays of MCs. In addition, the mechanism of fluorescence determination in MCs is introduced, including photoinduced electron transfer (PET), fluorescence resonance energy transfer (FRET), and inner-filter effect (IFE). Finally, we discussed the level of development and limitations of existing fluorescent nanotechnologies and suggested future possibilities in the detection of MCs. Florescence methods based on different nanomaterials can rapidly and accurately determine MCs in aqueous solution-related matrices, but the complexity of the environments relevant to the seafood and aquaculture chain limits the practical performance. The future development of multifunctional nanomaterials is needed to achieve a more stable and efficient portable method for the detection of MCs.