Microcysin (MC)， as one of the most toxic hepatoxins， is often detected in polluted water bodies， which seriously threatens the safety of drinking water for humans and animals. It is very important to develop its rapid detection methods. In the previous study， an anti-MC-LR phage display nanobody library was successfully constructed. In this study， using MC-LR-OVA as the coating antigen， the anti-MC-LR nanobody M110 was selected by four rounds solid phase biopanning. M110 could recognize MC-LR with good stability. Further， an indirect competiitive enzyme-linked immunosorbent assay (ic-ELISA) for the detection of MC-LR was established， with the half-maximal inhibitory concentration (IC50) of 3.55 ng/mL. The detection limit was 0.65 ng/mL and the linear range was 1.28-9.88 ng/mL. The correlation coefficient of ic-ELISA and UPLC-MS/MS was 0.998， indicating the M110-based ic-ELISA method has high accuracy and can be used for the actual detection of MC-LR residues in water sample.