Salinity is an important environmental factor that induces oxidative stress in shrimp. This study evaluated the effects of abrupt low-salinity stress (23, 17, and 11) on histological structure, lipid peroxidation, mRNA levels and activities of antioxidant enzymes, and gene expression of Nrf2-Keap1 signaling molecules at different times (6, 12, 24, 48, and 96 h) in the gills and hepatopancreas of Marsupenaeus japonicus. Mild or strong increase in the levels of nuclear factor erythroid 2-related factor-2 (Nrf2) and antioxidant genes and enzymes such as superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPX) were observed after short-term exposure (6 and 12 h). After 48 and/or 96 h of exposure to low salinity, Nrf2 was significantly downregulated (P < 0.05), which was accompanied by downregulation of the levels of Nrf2-Keap1 pathway-related genes and enzymes such as SOD, CAT, and GPX, along with upregulation of Kelch-like-ECH-associated protein 1 (Keap1) and malondialdehyde (MDA). Pathological alterations were also observed in the gills and hepatopancreas of M. japonicus after 96 h of exposure to different salinities. The observed changes in antioxidant gene expression are consistent with a requirement for Nrf2 in the induction of antioxidant genes. Furthermore, there was a negative correlation between the mRNA levels of Nrf2 and Keap1, indicating that Keap1 is important for inhibition of the Nrf2 response. Negative relationships were observed between lipid peroxidation and antioxidant enzyme activities, while positive relationships were observed between activities and gene expression levels of antioxidant enzymes, suggesting the changes in molecular and enzyme activity levels may provide protection against damage from low-salinity stress. In conclusion, our data demonstrated that Nrf2-Keap1 signaling is important for modulating the gene expression levels of antioxidant enzymes. This is the first study to elucidate the effects of low-salinity stress on antioxidant responses in M. japonicus through the Nrf2-Keap1 pathway. The results provide insights into the mechanisms by which crustaceans resist salinity stress.