Simplicity, sensitivity and high throughput are the qualities researcher always difficultly pursue in the screening surveillance assay for food contaminants. Herein, coupled with a common gel imager as a signal reader, a novel magnet-actuated droplet microfluidic immunosensor without any complicated manipulation system was successfully fabricated for the convenient and sensitive detection of cyanobacteria toxin microcystin-LR (MC-LR) in aquatic products. The proposed sensor demonstrated three superiorities compared to the extensively used microfluidic systems: 1) simple but effective operation only by magnetic force rather than inconvenient actuating devices; 2) high throughput parallel detection on a 15-channels chip; 3) convenient signal readout on an ordinary laboratorial gel imager. This gel imager-assisted magnet-actuated droplet microfluidic immunosensor exhibited a limit of detection as low as 6.0 × 10−4 μg/L with high specificity. The average recoveries were ranged from 92.0% to 96.6% in spiked fish and prawn samples, and showed a good agreement with confirmation method LC-MS/MS, suggesting the proposed method to be an ideal surveillance assay tool for the MC-LR monitoring in aquatic products.