As an important component of arid ecosystems, groundwater plays an important role in plant growth. We used the unsteady flow theory as the method, residual error function erfc(x) as the solution function, and time lag effect of groundwater depth change and phreatic evaporation as the basic condition to construct a monthly average groundwater depth change model from 2011 to 2015 of the lower reaches of the Tarim River Yingsu-section based on intermittent water conveyance. The results indicated that:First, during the period of ecological water conveyance, groundwater depth near the river channel fluctuates greatly in a short time, whereas fluctuation in groundwater depth was not greatly affected far from the river. This shows the influence of ecological water transport on groundwater depth near the river bank, which has a certain lag period, and the lag time increases gradually as distance from the river increases. Among all monitoring wells, the C4 monitoring well showed the shortest lag period, whereas the C7 monitoring well showed the longest lag period. Second, the unsteady flow of groundwater and phreatic evaporation were the most sensitive factors influencing the change in groundwater depth. The action of unsteady flow showed the greatest influence on groundwater depth during monthly variation and annual variation. The effect of phreatic water evaporation on the change in groundwater depth was small in the short term; however, the total influence of groundwater depth over many years cannot be ignored. Third, in core monitoring of the lower reaches of Tarim River, Populus-Tamarix chinensis-meadow mixed zone, meadow, meadow-desert mixed zone, and semi-desert were observed within 1050 m of the Yingsu-section, which require different groundwater depth. The simulation of groundwater depth changes in the lower reaches of Tarim River are based on the unsteady flow theory, with fitting accuracies (R²) at 300, 500, 750, and 1050 m of 0.701, 0.654, 0.701, and 0.625, respectively. These values meet the requirements for groundwater simulation accuracy and have important theoretical significance and reference values for studying relationships between groundwater and vegetation restoration in the lower reaches of Tarim River. This research will provide a reference for the simulation of groundwater level in arid area, which can be used to simulate the change of groundwater level at any location within the influence range of the river. Further exploration will improve the efficiency of ecological evaluation at a certain extent.