AbstractThe aim of this work was to extract, isolate, and purify polysaccharides from the heads of Hypomesus olidus and to evaluate their anticoagulant activities and anticoagulant mechanisms. Response surface methodology was used to optimize the extraction conditions for ultrasonic‐assisted extraction of polysaccharides from the heads of Hypomesus olidus. The optimal extraction conditions consisted of ultrasonic power of 275 W, ultrasonic time of 50 min, and solid–liquid ratio of 5 ml/g, giving the yield of crude polysaccharides (GYT) of 7.73 ± 0.042%. Three polysaccharide fractions, GYT‐1, GYT‐2, and GYT‐3 were purified from GYT by using DEAE‐cellulose‐52 column and Sephadex G‐100 column for anticoagulant activities. The results showed that two doses (2 and 4 mg/ml) of GYT‐1 and GYT‐3 could significantly prolong (p < .01) in partial thromboplastin time (APTT) (2.19 and 2.37 times, 2.22 and 2.44 times, respectively) and thrombin time (TT) (2.39 and 2.46 times, 2.44 and 2.80 times, respectively) compared with normal control. In particular, GYT‐3 had stronger anticoagulant activity than GYT‐1, and it was composed of arabinose, fructose, glucose, and lactose with molar ratios of 0.595:1: 2.026:0.273. However, GYT‐2 had no anticoagulant activity (p > .05). In addition, anticoagulation mechanism of polysaccharides from the heads of Hypomesus olidus (GYT‐3) was evaluated. The results showed that the anticoagulant activity of GYT‐3 was based on their binding with antithrombin AT‐III. And the inhibitory effects of GYT‐3 on factor IIa and Xa were related to the concentration of AT‐III in plasma. This study may provide a new and promising anticoagulant drug.