The interaction between plant species is realized through the direct or indirect influence of related microorganisms. The interaction between leguminosae and non-leguminosae is an ideal model for studying the relationship between plant species, but nitrogen fixation and microecological processes in the interaction between them are not well understood. In this study, the effects of plant interactions on nitrogen fixation and rhizosphere microorganisms in different habitats-field and plot-were studied, taking Alhagi sparsifolia Shap. (Legume) and Karelinia caspia (pall.) Less (Asteraceae) as the research objects. The study shows that those two species have nitrogen transfer characteristics in the field or in the plot, and the nitrogen transfer characteristics are more obvious in the field. In field habitat, the nitrogen transferred from Alhagi sparsifolia to Karelinia caspia accounted for approximate 50% of the total nitrogen in Karelinia caspia, while in the plot experiment it only accounted for approximate 30%. The interaction changes the stoichiometric ratio of different tissues of Karelinia caspia, and the proportion of nitrogen content in leaves increased under the interaction condition. In addition, the interaction between Alhagi sparsifolia and Karelinia caspia decreases Shannon index of rhizosphere bacterial community of Alhagi sparsifolia, and the interaction changes the gene function of the soil bacteria in the rhizosphere of Alhagi sparsifolia. The interaction has no significant effect on rhizosphere microbial community of Karelinia caspia. But gene abundance involved in nitrogen transportation in the rhizosphere is significantly higher than that in the single planting, among which the interaction has the greatest effect on the diversity of bacteria and gene function in the fine root rhizosphere of Alhagi sparsifolia. Moreover, the nitrogen content of fine roots of Alhagi sparsifolia is decreased by the interaction. Therefore, the Alhagi sparsifolia fine root could be the crucial part during the interaction between Alhagi sparsifolia and Karelinia caspia. This study provides a scientific basis for the protection and restoration of desert vegetation.