Because of global warming, desertification is increasing. One of the best strategies for combating desertification is reforestation of forests and biological operations of vegetation. However, events like soil salinity and dust storms, as the most important manifestations of desertification, prevent vegetation from settling in these areas. In this study, the effects of two halotolerant plant growth-promoting rhizobacterial strains, Bacillus pumilus HR and Zhihengliuella halotolerans SB, on physiological and nutritional status of the desert halophyte Haloxylon aphyllum under the stress of salinity (0, 300, and 600 mM NaCl) and dust (0 and 1.5 g m−2 month−1) were examined. Under dust application, the Z. halotolerans SB strain compared to the B. pumilus HR strain and the combination of these two bacterial strains improved the content of total chlorophyll (247 and 316%), carotenoid (94 and 107%), phosphorus (113 and 209%), magnesium (196 and 212%), and total dry biomass (13 and 28%) in H. aphyllum at salinity levels of 300 and 600 mM NaCl, respectively. Under conditions of combined application of dust and salinity, B. pumilus HR compared to Z. halotolerans SB and the combination of two strains at salinity levels of 300 and 600 mM NaCl, respectively, had better performance in increasing the content of iron (53 and 69%), calcium (38 and 161%), and seedling quality index (95 and 56%) in H. aphyllum. The results also showed that both bacterial strains and their combination were able to reduce the content of ascorbic acid, flavonoid, total phenol, proline, and malondialdehyde, and catalase activity, and ultimately improve the antioxidant capacity of H. aphyllum. This showed that the use of halotolerant rhizobacteria can stop the production of free radicals and thus prevent cell membrane damage and the formation of malondialdehyde under salinity and dust stress. The results of this study for the first time showed that halotolerant rhizobacteria can increase the seedling quality index of H. aphyllum under combined conditions of salinity and dust. The use of these bacteria can be useful in the optimal afforestation of H. aphyllum species in arid and semi-arid ecosystems.