As a hypertoxic natural toxin, the risk of Microcystin-leucine-arginine (MC-LR) residues in Bellamya aeruginosa deserves more attention. Herein, employing the conventional thin-layer chromatography (TLC) technology and a novel surface-enhanced Raman scattering (SERS) substrate, a TLC-SERS chip was fabricated for the purification and quantitative detection of MC-LR in complex samples. The substrate exhibited excellent SERS performance with an enhancement factor of 6.6 × 107, a low detection limit of 2.27 × 10−9 mM for MC-LR, excellent uniformity and reproducibility, as well as a wide linear range. With the application of TLC, the MC-LR was efficiently purified and the concentration was increased to >3 times. Ultimately, recovery rates fluctuated between 93.28% and 101.66% were obtained from the TLC-SERS chip. On balance, the TLC-SERS chip has a robust capacity for achieving rapid and stable quantitative detection of MC-LR, which promises to improve the efficiency of food safety monitoring.