Lignocellulosic hydrolysate contains several inhibitors that hinder downstream biological processes. The immobilized strain Burkholderia sp. H-2 was used in this study to biodetoxify real rice straw hydrolysate and biotransform 5-hydroxymethylfurfural (5-HMF), an inhibitor, into 2, 5-furandicarboxylic acid (FDCA), a valuable platform compound. An electrodialysis with bipolar membranes (EDBM) system was applied to recover FDCA and perform secondary detoxification of the biodetoxified real rice straw hydrolysate. The rice straw hydrolysate after biodetoxification and EDBM treatment was used for anaerobic dark fermentative hydrogen production. The immobilized Burkholderia sp. H-2 could completely biotransform 1843 mg/L 5-HMF into 1532 mg/L FDCA within 24 h when the 2-fold diluted rice straw hydrolysate was used as the feedstock. The optimal EDBM system parameters to recover FDCA were a hydrolysate pH of 6, operated at a current density of 17.86 mA/cm2. The FDCA recovery efficiency was 44.6 %, when using the biodetoxified real rice straw hydrolysate as the EDBM feedstock. The rice straw hydrolysate after biodetoxification and EDBM treatment had better biohydrogen production performance than the undetoxified and biodetoxified rice straw hydrolysates.