The desalination of fermented broth containing 1,3-propanediol by ion exchange coupling with electrodialysis was studied. Based on the laboratory-scale desalination experiment, the electrodialytical desalination, ion exchange resin, and the coupling process were also investigated. It is showed that the 1,3-PDO loss was 11.41% by electrodialysis. Among various cationic and anionic resins, LSI296 and LSI010 were used to pilot level by comparing pH, conductivity and exchange volume. The efficiency of desalination was improved to 96.2%, and the loss of 1,3-PDO was decreased to 5.88% by ion exchange coupling with electrodialysis.