It is rather difficult to separate high concentration of ammonium thiosulfate from ammonium thiocyanate in coking wastewater which results in resources waste and environment pollution. In this work, a membrane process of nanofiltration (NF) was applied to solve the problem. The experimental results showed that the NF membrane selectively retained (NH 4) 2S 2O 3 with a rejection of 95.0% at a concentration of more than 60 g L − 1 . Meanwhile, the permeation of NH 4SCN was 120.0% at a concentration of nearly 120 g L − 1 . Diafiltration was optimized to ensure a high average salt rejection of 93.4% for (NH 4) 2S 2O 3. In addition, salt concentrations and yields can be predicted by theoretical calculation. The results reveal that the NF membranes are successful in separating high concentration of bi-component ammonium salt solutions into mono-component ones.