The invention discloses a method for extracting paralytic shellfish toxins from shell tissues. The method comprises the following steps: 1, mixing shell raw materials with acetic acid until the pH value of the obtained mixture is 2-4, carrying out ultrasonic crushing, heating the crushed mixture in boiling water for 5-10min, cooling, filtering, and collecting the obtained filtrate; 2, carrying out reduced pressure concentration on the filtrate, freezing, centrifuging, taking the obtained supernatant, extracting the supernatant by using trichloromethane, uniformly mixing the obtained upper layer extract liquid with ethanol, stirring at room temperature for 20-24h, carrying out secondary centrifuge, collecting the obtained new supernatant, carrying out reduced pressure concentration, drying, dissolving the obtained dried material in acidic methanol, filtering, collecting the obtained new filtrate, drying, dissolving the dried new filtrate in an aqueous acetic acid solution with the pH value of 2-4, adding the obtained sample to a gel column, carrying out column chromatography, and collecting the fraction with the retention time of 160-250min. The method maximally improves the extraction rate of the paralytic shellfish toxins, can effectively remove fats, proteins, carbohydrates and other impurities in the tissues, and maximally reduces the bioactive loss of the toxins.