In this paper, the species diversity and the change of groundwater level in the lower reaches of Tarim River are analyzed and calculated based on the field-collected data from 40 observation wells of groundwater level along 9 sections and 8 plant plots in the lower reaches of Tarim river. The study shows that the species diversity is closely related to the change of groundwater level in the lower reaches of Tarim river, and the groundwater level plays a dominant role in the species diversity. In the lower reaches of Tarim River, the shallow groundwater level is deep, and it becomes deeper gradually from the upper reaches to the lower reaches, i.e.there is an obvious increase in the depth of groundwater. The index of species diversity is small in the lower reaches of Tarim River, and the Shannon-Weiner index and Simpon index vary in ranges of 1.93~0.53 and 0.82~0.35 respectively. Along with the increase of groundwater depth from the upper reaches to the lower reaches of Tarim River, the plant species become less, the structure of plant communities becomes simpler, and the diversity index and abundance index of the species are in an obvious decrease status. All these reflect the serious impacts of moisture stress on the ecosystems in this arid area.