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Microcystin LR (MC-LR) is a hazardous cyanotoxin produced by cyanobacteria during freshwater eutrophication, which can cause liver cancer. Here, a photoelectrochemical (PEC) aptasensor based on methylene blue (MB)–loaded Ni-MOF composite (Ni-MOF/MB) with spatial confinement was constructed for the sensitive detection of MC-LR. Ni-MOF with two-dimensional sheet structure was prepared via a liquid–liquid interface synthesis method with environmental-friendly solvent and milder reaction conditions. Benefiting from the uniform pore size, Ni-MOF acted as reaction platform to anchor the photosensitive molecule MB. The electron donor, ascorbic acid (AA), was produced by alkaline phosphatase (ALP) loaded on DNA strand catalyzing ascorbic acid phosphate. The generated AA was absorbed by Ni-MOF/MB, thereby effectively improving the utilization of AA and avoiding the external environment interferences to enlarge the photocurrent of MB. For analysis, ALP-labeled aptamer can specifically recognize MC-LR by forming a complex to strip from aptasensor, thus leading to a decreased photocurrent. The developed PEC aptasensor offered a linear range of 10 fM–100 pM with a detection limit of 6 fM. It was successfully employed for detecting MC-LR in farm water and fish meat, and the results were validated by ultrahigh-performance liquid chromatography-mass spectrometry. This method presents a new idea of MOF-limited domain for PEC aptasensing. [ABSTRACT FROM AUTHOR]