The invention discloses a rapid microcystin extracting and detecting method comprising the following steps: firstly, conducting pretreatment on algae samples, removing impurities on microcystis flosaquae samples, cleaning the microcystis flosaquae repeatedly by distilled water, and filtering the microcystis flosaquae; secondly, conducting homogenate process and heavy weight measurement, adding algae slurry concentrated in the step one into the distilled water, stirring the slurry uniformly by a homogenizer, taking the algae slurry additionally for measuring the dry weight; thirdly, extracting toxin by methanol one-step method, calculating the measuring result of dry weight of samples in the step two, taking the algae slurry with known dry weight and volume, stirring, vibrating and mixing the algae slurry, then standing and extracting the algae slurry in a refrigerator; fourthly, conducting centrifugal purification, conducting centrifuge on extracted liquid processed in the step three, obtaining supernate, and obtaining clarified extraction liquid; fifthly, using a filter for filtering the supernate obtained from the step four; sixthly, conducting HPLC (High-performance liquid chromatography) detection, adopting optimized chromatograph condition for analyzing the toxin rapidly. The method has the advantages of high reliability, simple needed instrument, convenience in operation, high detection efficiency and the like, and is suitable for large-batch toxin extraction and analysis in a laboratory.