In order to investigate the effects of salinity and magnesium (Mg) on the growth parameters, physiological characteristics and content of some metabolites in Syrian bean-caper (Zygophyllum fabago) plants, a factorial experiment with completely randomized design was performed and carried out in perlite with Hoagland solution. The treatments were combinations of two levels of salinity (0 and 300 mM NaCl) and three levels of Mg concentration (2, 4 and 8 mM; 0, 2 and 6 mM over the standard Mg content of Hoagland medium, 2mM, respectively). The simultaneous effect of salinity and Mg did not change the fresh weight of the plants, but increased the dry weight by 50%. Salinity reduced the leaf area, but the presence of Mg improved and even increased the leaf area of the plants. The Mg reduced NAR, while increased LAR and RLGR. Salinity decreased the RLGR. The simultaneous effect of salinity and Mg increased and improved RGR, LWR, RLGR. The tolerance index in saline treatments increased with the presence of Mg, but the R/S ratio showed a significant increase only in salinity condition, however, the presence of Mg moderated it. Salinity reduced the photosynthetic pigments, while the presence of Mg ameliorated the decrease. As a result, salinity and Mg increased the total sugar content of the leaf and reduced the total sugar content of the root. Salinity and Mg reduced the total protein content of all the organs of the plant specimens studied. In general, salinity had a negative effect on the physiological parameters of the Zygophyllum fabago plants, while the application of supplementary Mg improved the growth indices and increased the plants tolerance against salinity.