Suaeda salsa is a native halophyte in saline soils. Salinity is the most important environmental constraint for plant productivity in the Yellow River Delta. In this work, we investigated the salt-induced effects in root of S. salsa exposed to two environmentally relevant salinities for 1 week and 1 month using nuclear magnetic resonance-based metabolomics. Our results indicated that salt stress inhibited the growth of S. salsa and induced significant metabolic responses including decreased amino acids, lactate, 4-aminobutyrate, malate, choline, phosphocholine, and increased betaine, sucrose, and allantoin in root tissues of S. salsa. In addition, salinity exposures upregulated the activities of superoxide dismutase, glutathione S-transferases, peroxidase, catalase, and glutathione peroxidase in the aboveground part of seedlings of S. salsa after exposures. Overall, these results demonstrated the osmotic and oxidative stresses, disturbances in protein biosynthesis/degradation, and energy metabolism in S. salsa exposed to salinities.