The Fe3O4@NiSiO3 magnetic nanoparticles（NPs） were prepared by hydrothermal synthesis and sol-gel method.The nanoparticles microspheres have uniform morphology，good magnetic properties and dispersion.In this study，the synthesized NPs as a magnetic solid phase extraction（MSPE） media were combined with high performence liquid chromatography（HPLC） to develop an effective method for the detection of trace microcystin-LR（MC-LR） in water samples.After optimizing the MSPE and HPLC chromatographic conditions，the method showed a good linear relationship in the range of 0.25-146.5 μg/L with correlation coefficient（r） of 0.999 1.The detection limit was 0.011 μg/L.The method was applied in the analysis of microcystin toxins in pure water sample and actual water samples with recoveries of 81.0% and 66.7%-72.0%，respectively.The results showed that Fe3O4 @NiSiO3 magnetic nanoparticles have good enrichment capability，and could be effectively used for the extraction of trace microcystin in water.