[Background] The Ebinur Lake wetland national nature reserve in Xinjiang is one of the most representative temperate arid regions wetland desert ecosystems in China, and plays an important role in maintaining regional ecological balance. At present, there has not been any report on the structure and abundance of nitrogen-fixing microorganisms in rhizosphere and non-rhizosphere soil at Ebinur Lake wetland. [Objective] To explore the characteristics of environmental heterogeneity of community structure and abundance of nitrogen fixation gene (nifH) in the soil rhizosphere and non-rhizosphere soil nitrogen-fixing microbial of Halocnemum strobilaceum in Ebinur Lake wetland in Xinjiang. Based on this, the potential forces of the microbial communities in the desertification and continuous salinization of the Ebinur Lake wetland ecosystem in the temperate arid regions are explored, providing the theoretical and data basis for the degradation and restoration of lake wetlands. [Methods] The correlations among soil physicochemical properties, microbial community structure and microbe abundance were investigated by using the methods of constructing clone library, q-PCR and redundant analysis (RDA). [Results] The results showed that the diversity of nifH gene in non-rhizosphere soil were higher than that in rhizosphere soil. The dominant species of nifH sequence were Azorhizobium and Desulfovibrio in the rhizosphere soil, Azoarcus, Heliobacterium modesticaldum and Desulfovibrio in non-rhizosphere soil. The number of nifH gene was 4.08×104 copies/g in rhizosphere soil and 5.52×103 copies/g in non-rhizosphere soil. The abundance of nifH in rhizosphere soil is higher than that in non-rhizosphere soil. Correlation analysis showed that the dominant groups and abundance of containing nifH bacteria in rhizosphere soil were significantly related with nitrate nitrogen (NO3?-N), available nitrogen (AN), total potassium (TK), soil moisture (SM) and other factors, and with nitrate nitrogen (NO3?-N), available nitrogen (AN), total phosphorus (TP), total potassium (TK) and total nitrogen (TN) in non-rhizosphere soil. [Conclusion] These results indicated that the abundance of nifH bacteria in rhizosphere soil was higher than that in non-rhizosphere soil, while the diversity was lower than that in non-rhizosphere soil. Nitrate nitrogen (NO3?-N), available nitrogen (AN), total phosphorus (TP) may affect the community structure and abundance of nitrogen-fixing microorganisms. These characteristics provide the theoretical and data basis for the degradation and restoration of lake wetlands.