The MC-LR from the the blue-green algae of Taihu Lake was extracted, at the same time, a set of microcystins extraction method with methanol as extraction solvent and purification method with C18-SPE as purification workstations were established. The extraction solvent concentration, extraction time, extraction solvent amount, leacheate concentration and eluent concentration were used to research the extraction efficiency of MC-LR. Finally, 80% methanol was used to wash microcytins to make MC-LR high purity and the purity was over 85%. This research presented a method of low cost and high efficiency. It provided the foundation for the further research of microcytins.