Herein the extraction method of fucoidan from Laminaria japonica is reported. Firstly, chitosan, chitosan-N-2-hydroxypropyl trimethyl ammonium chloride (HACC), and hexadecyltrimethylammonium bromide (CPAB) were used to extract the fucoidan. The results showed that chitosan was the optimal extractant compared with the other two extractants. After extraction, different aqueous solutions, including NaCl, KCl, and HCl (pH2), were used to separate fucoidan from chitosan-fucoidan complex. The results showed that the separation ability of NaCl was slightly higher than that of KCl. Moreover, the price of NaCl is lower than that of KCl. Given the quality-price rate, NaCl solution was chosen as the separation solution. Thirdly, the concentration and ratio of NaCl solution : sediment influence the separation of fucoidan from chitosan-fucoidan complex. The results showed that the optimal separation conditions include 4 mol/L NaCl solution with the ratio of NaCl solution to sediment at 30 : 1. Fucoidan content was found to be affected by different separation time. Fucoidan content increased with the increase of separation time, and the optimal separation time was 6 h. Compared with traditional alkali extraction method, this method not only reduces the usage of alkali and acid and alleviate environment pollution, but also has the comparable extraction yield of fucoidan. It is a potential method for extraction of fucoidan.