Microcystins (MCs) is one of the most commonly toxic cyclic heptapeptide cyanotoxins with a variety of congeners in aquatic environments. Different MC congeners exhibit different toxicity
however, successful discrimination of MC congeners in complex samples remains challenging. Herein, we combine efficient enrichment of magnetic imprinting and precise discrimination of fluorescence sensor arrays, constructing a new strategy to distinguish MC congeners (MC-LR, MC-RR, and MC-YR). Based on phosphate-guanidine oriented surface imprinting and dummy template imprinting strategy, the prepared magnetic molecularly imprinted materials demonstrated excellent adsorption and selectivity for each MC congeners. The material enriched three MCs simultaneously and eliminated the complex matrix interference in water samples, laying a foundation for array sensing. Finally, a three-unit sensor array was constructed using fluorescent materials interacting with congeners to generate response signals, providing fingerprint patterns to distinguish MCs. Linear discriminant analysis (LDA) processed the fluorescence spectral data, demonstrating 100 % accuracy in differentiation and quantitative discrimination of congeners and their complexes. Combing the advantages of efficient enrichment of magnetic imprinting and precision distinction of fluorescence sensor arrays, the practical application of this method demonstrated good performance in discriminating MCs in real environmental samples.