Based on the monitoring data of 36 groundwater-monitoring wells and vegetation plots in the lower reaches of the Tarim river from 2004 to 2006, the characteristics of species diversity was analyzed by using the formulas of Margalef′s richness indices, Shannon-Weiner′s indices, Atalato′s evenness indices, correctional Simpson′s indices and the Hill indices. The results showed that the species diversity is closely related to the groundwater table and the groundwater plays a dominant role in the species diversity in the lower reaches of Tarim river. Along with the increase of groundwater depth from the upper reaches to the lower reaches of the monitoring sections of the Tarim River, the plant species become less, the structure of plant communities becomes simpler, and both the diversity and richness index of the species are in an obvious decrease status. The evenness indices, however, didn′t show the same change trend. The Hill species diversity indices showed that the species diversity has distinct changing characteristics at the groundwater depth among 2-6m，6-10m and >10m. Once the depth of groundwater lower than 6 meter, the diversity values become small and the trend of diversity curve becomes smooth. Combining the field investigation and the analysis of the plots, it is considered that the critical groundwater depth for the damaged species diversity is about 6 meter in the lower reaches of the Tarim River.