Using one-year Haloxylon ammodendron transplants growing in the south part of the Gurbantunggute Desert, we investigated the aboveground growth, diurnal transpiration rate change and root morphology of H. ammodendro seedlings, and explored the growth and adaptation characteristics of H. ammodendron seedlings in different habitats (windward slope, leeward slope, and inter-dune lowland). The results showed that there was no significant difference in soil moisture contents of the 0-30 cm soil layer among different habitats, while the soil moisture contents of 40-100 cm soil layer were significantly different among the three haitats, 6.65%-13.60% at the leeward slope, 1.91%-3.56% at the windward slope, and 3.43%-3.59% at inter-dune lowland. Water content and growth rate of the assimilating shoots of H. ammodendron seedling at different habitats performed as similar as the soil moisture content, suggesting that water content and growth rate of the assimilating shoots could probably be related to soil moisture. The diurnal transpiration rate change of H. ammodendron seedlings at different aspects showed a similarly single-peaked type, with significantly higher diurnal water consumption at the windward slope than that at the leeward slope and the inter-dune lowland during 12:00-16:00. The axial root of H. ammodendron seedling at the windward slope was poorly developed, with many but short lateral roots. Whike the axial roots at the inter-dune lowland and the leeward slope were highly developed, with one single axial root, which implied that the root system could adapt itself to the soil moisture under corresponding habitat.