Cylindrospermopsin (CYN) can bioaccumulate in aquatic food chains and cause potential toxicity to human and animal health. When analyzing biological samples using liquid chromatography with tandem mass spectrometry (LC-MS/MS), the presence of complex matrices is a major concern. In this study, we developed a novel immunoaffinity extraction method for CYN enrichment in different biological matrices. Magnetic beads bound with a monoclonal antibody against CYN were used as affinity probes to specifically enrich CYN in samples, which effectively eliminated matrix effects for LC-MS/MS analysis. Under optimized conditions, the automated method processes 32 samples in 54 min without any centrifugation or filtering steps. When coupled to LC-MS/MS, this new method shows excellent sensitivity (LOQ, 0.025 μg L-1), linearity (R2 > 0.99, 0.125-100 μg L-1), precision (RSD < 6%), and recoveries (85-105%). Using the established method to measure CYN contents in 10 muscle and liver tissue samples of fish from a reservoir of southern China, we found its analogue deoxy-cylindrospermopsin (deoxy-CYN) was detected more frequently and also with higher concentration than CYN. An average concentration of 2.38 μg kg-1 in muscle and 71.99 μg kg-1 in liver suggested that CYN accumulation is highly tissue-specific. This is the first report of immunoaffinity extraction for CYN enrichment. Our results demonstrate that the developed method is reliable and offers significant application prospects.