Microcystins (MCs), a family of cyclic heptapeptide cyanotoxins, exists in aquatic environment where cyanobacterial bloom happens, which will accumulate in aquatic organisms and transfer through the food chain to higher trophic levels, posing a health risk to both animals and human bodies. Among various MCs, Microcystin-LR (MC-LR) is worthiest studied for its strong toxicity, ubiquity and widespread. Here in this work, iminodiacetic acid (IDA) decorated magnetic mesoporous silica (mSiO2) nanocomposites (Fe3O4@mSiO2-IDA) were facilely synthesized which possessed the merits of large surface area (188.21 m²/g), accessible porosity (2.66 nm), excellent hydrophilicity and rapid responsiveness to magnetic field. Then the composites were successfully employed to the removal process of Microcystin-LR in real water samples followed by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, achieving the removal efficiency above 92.5% even after ten recycles of the composites. It provided a potential method for removing MC-LR in aqueous environment with high effectiveness, lower costs and less secondary contamination.