Understanding the relationships among species is central to ecological research, however, many knowledge gaps remain regarding how desert plant species interact. In the present study, we assessed the effect of rainfall on the belowground interactions and root morphology of two desert shrubs, Reaumuria soongorica (Tamaricaceae) and Salsola passerina (Chenopodiaceae), from three communities with similar landforms and soil environments. The roots of both R. soongorica and S. passerina were deeper when grown together than grown singly. Interestingly, the belowground biomass of R. soongorica was higher but the belowground biomass of S. passerina was lower when grown together than when grown alone. This suggests that S. passerina benefitted from the association with R. soongorica. When grown together under conditions of low rainfall, the roots of R. soongorica were deeper than those of S. passerina, which suggests that R. soongorica is more robust than S. passerina when subjected to periods of decreased rainfall. We concluded that the symbiotic relationship between these two shrub species can lead to deeper roots and that the plants are affected by rainfall availability. Combined with the output results of climate change models, we speculated that the distribution area of these two species will expand to the west, which has important implications on how the interactions of other desert species may change in response to climate variability.