The present invention provides a method for extracting ε-polylysine (ε-PL) and its hydrochloride salt from fermentation broth, which belongs to the field of bio-separation engineering. ε-PL and its hydrochloride salt are produced from fermentation broth through sequential solid-liquid separation, ultrafiltration, two-stage ion exchange, nanofiltration, evaporation concentration and drying techniques. Technologies of membrane filtration and two-stage ion exchange are applied to the preparation of ε-PL and its hydrochloride salt in the present invention, and the invention are characterized by reduced cost, improved automation, and increased product yield and purity, and the method of the present invention would be more suitable for industrial production.