This paper takes the ecological water conveyance project (EWCP) that transfers water from the Bosten Lake, to Daxihaizi Reservoir, and finally to the Taitema Lake as a case study to analyze the dynamic change of the groundwater depth, the vegetation responses to the elevation of the groundwater depth as well as the relationship between the groundwater depth and the natural vegetation. The results from many years' monitoring in field indicate: (1) the groundwater depth has been elevating gradually with the increase in the times of watering and the elevation range has been expanding continuously in the lower reaches of Tarim River. Correspondingly, the natural vegetation has a favorable response to the elevation of the groundwater depth. The change of the natural vegetation has accordance with that of the groundwater depth. Such facts not only show that groundwater is a key factor to the growth of the native vegetation but also prove it is feasible that the degraded ecosystem can be restored and protected by the EWCP; (2) the results of analysis of the spatial-temporal response of the natural vegetation to watering reveals that the beneficial influence of the EWCP on the ecosystem in the lower Tarim River is a long-term process; (3) in terms of the function and structure of ecosystem after watering in the lower reaches of Tarim River, the EWCP does not still reach the goal of ecological restoration at a large spatial scale at present. Based on such monitoring results, some countermeasures and suggestions for the future restoration strategy are proposed so as to provide a theoretical basis for restoring and protecting the ecosystem in Tarim River, and meanwhile it can also provide some scientific references for implementing the similar ecological projects in other areas.