The invention discloses a method for separating and purifying microcystin by utilizing series-connected solid phase extraction columns. The method comprises the following steps of: A, preparing an algae powder material, namely harvesting wild bloom-forming cyanobacteria or microcystis aeruginosa cultured indoors, cooling and drying to prepare dried algae powder; B, preparing the solid phase extraction columns, namely putting C18 fillers into Solid Phase Extraction (SPE) columns; C, extracting algae toxin, namely weighing the dried algae powder, adding methanol according to a proportion, putting on a shaking table and oscillating at room temperature; D, removing impurities, namely adding a supernatant and an organic extractant into a separating funnel according to a proportion, mixing and uniformly shaking, standing, and after delamination, removing the organic extractant; E, separating and purifying the algae toxin, namely after pretreatment, enriching sample solution by using pre-activated series-connected SPE columns, and eluting the toxin by using 20 to 50 percent methanol aqueous solution; and F, performing Methyl Cellulose (MC) detection. The method has good separation effect, large loading amount, is easy and convenient to operate and low in cost, can obtain two microcystins with the weight of more than or equal to 10 mg and higher purity each time, and the High Performance Liquid Chromatography-Ultra Violet/Diode Array Detector (HPLC-UV/DAD) detection can reach 85 to 90 percent.