The interaction between plants and the environment, especially the interspecific associations in certain ecosystems, is an important ecological topic. The Kongque River originates from Boston Lake and flows through the east of the Taklamakan Desert; it plays a critical role in supplying water and ecological stability to the South Korla and Lop Nur regions. Owing to climate change, and excessive human exploitation, water availability has become increasingly limited, resulting in severe ecological degradation in the lower reaches of the Kongque River. Therefore, to evaluate the degree of ecological degradation and potential restoration probability in the lower reaches of the Kongque River, this study focused on the interspecific associations of the degraded desert riparian ecosystem by analyzing the groundwater, soil salinity, soil nutrients, and vegetation in 2013. The results showed that: 1) Based on the variation in groundwater depth, soil salinity, soil type, vegetation coverage, species richness, and species diversity, the longitudinal habitats in the lower reaches of the Kongque River could be divided into three types: oasis-desert ecotone, intermediate desertification zone, and saliniferous desertification zone. In the oasis-desert ecotone, the groundwater depth was soil salinity was low, Populus euphratica was the constructive species in plant community, vegetation coverage varied from 9.04% to 21.10%, and the soil was mainly formed by sandy loam. The groundwater depth, soil salinity, and soil texture in the intermediate desertification zone were similar to those in the oasis-desert ecotone. However, the vegetation coverage, species diversity, and species biomass were lower than those in the oasis-desert ecotone. Tamarix ramosissima Ledeb. and T. hispida Willd. were the constructive species of the plant community. The groundwater depth and soil salinity in the saliniferous desertification zone were the highest among the three zones, and sand grain factor affecting the soil. Owing to the severe environmental factors, P. euphratica and Tamarix spp. could not survive; therefore, the desert halophytes, such as Halostachys caspica C. A. Mey, and Kalidium foliatum Moq. were the constructive species in the plant community. 2) Overall, inter-specific associations between different species in the lower Kongque River were not significant. Most of the pairwise associations in the oasis-desert ecotone were positive. Nevertheless, associated coefficients were <1, which indicated that the ecological stability of the ecotone was vulnerable. The pairwise association in the intermediate desertification zone was not significantly negative, and the association coefficients were also <1. This finding implied that the environmental factors were highly heterogeneous, and the ecosystem was deteriorating. The pairwise association in the saliniferous desertification zone was significantly positive, and most of associated coefficients were >1, for all the survival species in this zone were euhalophytes. Consequently, the ecological degradation in this zone was the most serious. 3) A canonical correspondence analysis showed that in the oasis-desert ecotone, the key species, P. euphratica showed a positive association with other species, the habitat expressed characteristics of moderate soil salinity, high nutrients, and suitable soil moisture. Unlike the oasis-desert ecotone, associations among species in the intermediate desertification zone were not significant, the two key species, T. hispida and T. ramosissima, were interdependent, and the habitat was characterized as having lower soil nutrient and water contents. In the saliniferous desertification zone, associations among euhalophytes such as Kalidium foliatum, Halocnemum strobilaceum, and Karelina caspica were significantly positive, and the characteristics of the habitat were barren soil, a shallow groundwater level, and high salt salinity.