Understanding the effect of soil moisture on the growth of Populus euphratica seedlings' aboveground part and underground part is important to explain why its seed regeneration is difficult in natural conditions, and furthermore to increase the survival rate of seedlings. An experiment with two different watering treatments was carried out on the biennial seedlings of P. euphratica. The seedlings' aboveground growth indices (basal diameter, crown width, height, number of leaves) and underground growth indices (total root length, total root surface area per unit square meter of soil total root length, total root volume ) were monitored to analyze the effect of different watering treatments and water gradient on growth tradeoff of the seedlings. The results showed that, for the growth of aboveground parts of seedlings, a soil moisture content of 25% was optimum water condition under continuous watering, but under the intermittent watering treatment, a soil moisture content of 30% was most suitable. There was a significant difference in seedlings' underground growth under different watering treatments, and a soil moisture content of 25% was significantly different from other levels and more beneficial to root growth. After drought stress, the intermittent water supply was more favorable to root growth than the continuous water supply, and soil moisture content of 20% to 25% was more suitable to root biomass accumulation. When seedlings were subjected to drought stress, the accumulation of underground part biomass was more than that of aboveground parts, and the trade-off effect between the underground and aboveground growth was more conducive to the nutrients and water allocation to the longitudinal growth, but the lateral growth of roots was increased more with enough water supply.