The salt in the wastewater of the cephalexin enzymatic process was removed by electrodialysis. The influence of operating voltage, velocity ratio and temperature on the desalination process were investigated. The change of the permeate flux in the reverse osmosis separation process was also studied. The results showed that the electrodialysis process performed better in desalination with the organic matter retention rate reaching 99.50%, the energy consumption of 3.65KWh/kg at the conditions of the velocity ratio of 1:1, the operating voltage of 25V and temperature <30℃. During the reverse osmosis separation process, the decay of permeate flux was slow and acceptable, and the the water recovery rate was 75.67%. All results showed that it was feasible to treatment the waste water of the cephalexin enzymatic process by a combined process of electrodialysis and reverse osmosis.