Groundwater is an important and stable water source for desert vegetation due to the scarcity of precipitation in arid areas. Currently, anthropogenic withdraw of groundwater and climatic drought further limits the water availability for phreatophytic vegetation in arid regions and results in the decline of native vegetation. However, how phreatophytic plant response and adaptation to reduced water availability along the groundwater depth gradient are not clear. Haloxylon ammodendron was widely distributed in northwest arid zone of China and played an important role in desertification control. Groundwater was an important water resource for H. ammodendron. The declining groundwater depth has caused the partially decline even death of H. ammodendron in their native distribution area. In this study, we selected H. ammodendron, one of the main constructive species, at the southern edge of Gurbantonggut Desert as the taget species. In order to understand the response characteristics and regulatory adaptation mechanisms of desert plants to increasing groundwater depth and seasonal drought, we measured physiological and biochemical traits (including predawn water potential, midday water potential, water content, sodium ion, chloride ion, proline and non-structural carbohydrates), growth and morphological characteristics (including growth rate and Huber value) of assimilation branches in the early and late growing season under different groundwater depths (3.45, 9.08, 10.47, 13.27 and 15.91 m). The results showed that:(1) H. ammodendron adopted the strategy of first decreasing and then increasing predawn assimilation branch water potential, decreasing assimilation branch growth rate during new branch formation, increasing the Huber value and accumulating non-structural carbohydrates in response to increase in groundwater depth. (2) With the prolonged drought, H. ammodendron reduced predawn assimilation branch water potential, maintained high Huber values, accumulated sodium ions and consumed starch to resist seasonal drought during the growing season. (3) Reducing midday assimilation branch water potential, maintaining high assimilation branch water content and accumulating soluble sugars are ecological strategies in H. ammodendron to acclimate atmospheric and hydrological drought. In summary, there are differences in the physiological characteristics of H. ammodendron in response to groundwater hydrological drought and seasonally atmospheric drought. The results of the study enriched the knowledge of the effects of hydrological and atmospheric drought on the physiology and growth of H. ammodendron, and provided a reference for the conservation of desert vegetation based on groundwater resource management in arid areas.