Riparian plant diversity in arid regions is sensitive to changes in groundwater. Although it is well known that groundwater has a significant influence on plant diversity, there have been few studies on how groundwater and soil salinity impact plant community in desert riparian ecosystems. Therefore, we surveyed 77 quadrats (100 m × 100 m) to examine the relationship between groundwater depth, groundwater salinity, soil salinity and plant community in the upper reaches of the Tarim River. Data were analyzed with two-way indicator species analysis (TWINSPAN), detrended canonical correspondence analysis (DCCA) and principal component analysis (PCA). The results indicated that Populus euphratica, Tamarix ramosissima, and Phragmites australis were the dominant plants among trees, shrubs and herbs, respectively. Five plant community types were classified. There were significant differences in species diversity, soil moisture, soil salinity, groundwater depth and groundwater salinity across the community types. The composition and distribution of plant community are significantly influenced by groundwater depth, groundwater salinity, soil moisture, distances from the river to the quadrats, soil pH, electrical conductivity, total salt, CO32-, Cl-, SO42-, Ca2+, Mg2+, Na+ and K+. Shallow groundwater depth, low groundwater salinity, and high soil moisture and soil salinity were associated with higher plant diversity.