To explore Auricularia auricula-judae polysaccharides (AAP) as natural anticoagulants for application in the functional food industry, ultrasound assisted extraction (UAE) was optimized for the extraction of AAP by using a response surface methodology (RSM). The maximum extraction yield of crude AAP (14.74 mg/g) was obtained at the optimized extraction parameters as follows: Extraction temperature (74 °C), extraction time (27 min), the ratio of liquid to raw material (103 mL/g), and ultrasound power (198 W). Furthermore, the acidic AAP (aAAP) was precipitated with cetyltrimethylammonium bromide (CTAB) from crude AAP (cAAP). aAAP was further purified using ion exchange chromatography with a DEAE Purose 6 Fast Flow column to obtain aAAP-1. Additionally, according to the HPLC analysis, the aAAP-1 was mainly composed of mannose, glucuronic acid, glucose, galactose, and xylose, with a molar ratio of 80.63:9.88:2.25:1:31.13. Moreover, the results of the activated partial thromboplastin time (APTT), prothrombin time (PT), and thrombin time (TT) indicated aAAP-1 had anticoagulant activity, which was a synergic anticoagulant activity by the endogenous and exogenous pathway.