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Sensing Microcystin-LR (MC-LR) is an important issue for environmental monitoring, as the MC-LR is a common toxic pollutant found in freshwater bodies. The demand for sensitive detection method of MC-LR at low concentrations can be addressed by metasurface-based sensors, which are feasible and highly efficient. Here, we demonstrate an all-dielectric metasurface for sensing MC-LR. Its working principle is based on quasi-bound states in the continuum mode (QBIC), and it manifests a high-quality factor and high sensitivity. The dielectric metasurface can detect a small change in the refractive index of the surrounding environment with a quality factor of ~170 and a sensitivity of ~788 nm/RIU. MC-LR can be specifically identified in mixed water with a concentration limit of as low as 0.002 μg/L by a specific recognition technique for combined antigen and antibody. Furthermore, the demonstrated detection of MC-LR can be extended to the identification and monitoring of other analytes, such as viruses, and the designed dielectric metasurface can serve as a monitor platform with high sensitivity and high specific recognition capability.