Due to the current background of global climate change and heavy human activities, the precipitation and groundwater table on the southern edge of the Gurbantunggut desert have significantly changed, which could lead to variations in water use strategies of local plants. In our study, growth of the seedlings of Haloxylon ammodendron was investigated to reveal its growth traits and adaptability in the southern edge of Gurbantunggut desert. The results showed that the seedlings grew well from April to June when the soil water content was high, with the consumption of soil moisture, the above-and below-ground part of plant began to fall off, and then recovered growing in August. Mortality of seedlings showed a downward trend in the whole growth period. It suggested H. ammodendron seedlings could occupy more resource through rapid growth before the drought period, and falling of the assimilating branches in the drought period could maintain balance between water supply deficit and water consume of the assimilating organs. This morphological adjustment reduced seedlings mortality effectively. Also, more photosynthate was assigned toward root could ensure seedlings survival and recovered growth quickly at proper water conditions.