The invasion of native plants has posed a serious risk to species diversity and ecosystem function. How they modify underground community and facilitate successful invasion remain unknown. Soil diazotrophs may play an important role in invasion by native plants. Stellera chamaejasme L. has expanded within around the heavily degraded Horqin Grassland in northeast China in recent decades. This study aims to detect the effect of the expansion of S. chamaejasme L. on soil diazotrophic community structure through high-throughput sequencing and examine the relationship between diazotrophic community structure and soil physicochemical properties. An extensive increase in S. chamaejasme population induced significant changes in soil diazotrophic community and marked shifts in the relative abundances of Bradyrhizobium and Desulfuromonas. Soil organic matter (SOM), total nitrogen, NO3−-N, and electrical conductivity (EC) increased, whereas NH4+-N and pH significantly decreased in soil invaded by S. chamaejasme. The diazotrophic community structure was correlated with SOM, nitrogen content, EC, and pH. The relative abundances of Bradyrhizobium and Desulfuromonas were significant negatively and positively correlated with soil EC, respectively. This study suggests that the interaction between S. chamaejasme and soil diazotrophic microbes and the durative increase in soil EC may facilitate invasion by this S. chamaejasme population.