Electrodialysis (ED) was employed to remove the organic and inorganic salts from actual 1,3-propanediol (PDO) fermentation broth. These salts cause many problems during the purification of PDO if not removed. Suitable operation parameters such as applied potential and the flow rate of streams were selected to ensure a stable and durative desalination process for PDO fermentation broth. Under these conditions, the membrane fouling can be alleviated effectively by changing pole and cleaning membranes so that further industrial production is possible. The experiment results show that about 90% of organic acid salts in PDO broth are removed by the ED process. In addition, a simulated diffusion PDO experiment proved that the diffusion of PDO results in its loss from fermentation broth and the loss ratio is less than 6% under the chosen operating conditions.