Compared to the traditional desalination process, the effect of three-stage countercurrent gradient desalination on the quality of the pickled mustard tubers was studied. The results showed that the quality of the pickled mustard tubers treated by three-stage countercurrent desalination was better than others. It was found that the total radios of pickled mustard tubers and water was 1∶2(g/mL), 1∶1(g/mL), and 1∶1(g/mL) in the reaction level 3, 2 and 1, respectively, desalting for 3 min, and the level 1 was confirmed to be the best reaction among the three ones. In this case, the content of salt, total acid and total amino acid in the pickled mustard tubers were 6.0%, 3.4 g/kg, and 664 mg/100 g, respectively, and 53 kinds of flavor substances were detected. The content of salt, total acid and total amino acid in the final saline solution were 3.2%, 1.76 g/kg, and 80.3 mg/100 g, respectively. Therefore, the final saline solution could be used for the process of mustard tubers sauce. In conclusion, this desalination process turned out to be more effective than the traditional one, and the quality of the pickled mustard tubers in this reaction was better than those in others. Moreover, it could help to reduce the water consumption during the process and then could alleviate the pressure of sewage treatment.