As part of global climate change, variation in precipitation in arid ecosystems is leading to plant adaptation in water-use strategies; significant interspecific differences in response will change the plant composition of desert communities. This integrated study on the ecophysiological and individual morphological scale investigated the response, acclimation and adaptation of two desert shrubs, with different water-use strategies, to variations in water conditions. The experiments were carried out on two native dominant desert shrubs, Tamarix ramosissima and Haloxylon ammodendron, under three precipitation treatments (natural, double and no precipitation, respectively), in their original habitats on the southern periphery of Gurbantonggut Desert, Central Asia, during the growing season in 2005. Changes in photosynthesis, transpiration, leaf water potential, water-use efficiency, above-ground biomass accumulation and root distribution of the two species were examined and compared under the contrasting precipitation treatments. There were significant interspecific differences in water-use strategy and maintenance of photosynthesis under variation in precipitation. For the phreatophyte T. ramosissima, physiological activity and biomass accumulation rely on the stable groundwater, which shields it from fluctuation in the water status of the upper soil layers caused by precipitation. For the non-phreatophyte H. ammodendron, efficient morphological adjustment, combined with strong stomatal control, contributes to its acclimation to variation in precipitation. On account of its positive responses to increased precipitation, H. ammodendron is predicted to succeed in interspecific competition in a future, moister habitat.