Soy sauce is a traditional Chinese food condiment, normally containing a high concentration of sodium chloride (NaCl, 18–20%, w/v). To meet people's demand for healthy foods, part of NaCl needs to be removed from the raw soy sauce. In this study, nanofiltration was employed for the removal of salt and the recovery of nutritional components such as amino acid and fragrance from raw soy sauce, using four commercial NF membranes (NF270, NF-, NF90, Desal-5 DL). NF270 was found to be most suitable for the purpose. It was used to further study the effect of operation modes on desalination performance. The combination mode that concentration of the diluted soy sauce to its original volume, followed by diafiltration, was found to be most suitable one in terms of amino nitrogen (AN) and NaCl rejection, water consumption and operating pressure. Moreover, it was found that the rejection of AN was constant under the experimental conditions examined while NaCl rejection showed a linear relation with the concentration ratio of AN to NaCl. Based on mass balance and rejection equations, mathematical models were developed for predicting the concentration of solutes in retentate during desalination process, the simulation results agreed well with the experimental data.