Salinity is not only a threat to organisms and ecosystems, but also a major factor restricting the development of agricultural production. This study aimed to explore the modification effect of in-situ Jerusalem artichoke (genotype NY-1) cultivation on the rhizosphere micro-ecological environment in the saline-alkali region along the southeast coast of China. We analyzed the change of carbon and nitrogen in the saline soil from a microbial perspective, through the quantification of the area of root channels, rhizosphere secretions and soil microbiome (cbbL, cbbM and nifH). The root channels of NY-1 not only improved the physical structure of saline soil, but also provided a living space for microorganisms, afforded basic conditions for the optimization of the soil micro-ecological environment. In addition, rhizosphere secretions (from roots of NY-1 as well as microorganisms), such as carbohydrates, hydrocarbons, acids, etc., could be considered as a way to improve the saline-alkali soil habitat. NY-1 increased the diversity and abundance of autotrophic and nitrogen-fixing bacteria in saline soil (rhizosphere > bulk soils), which should be a biological way to increase the amount of carbon and nitrogen fixation in soil. Moreover, some of the detected genera (Sideroxydans, Thiobacillus, Sulfuritalea, Desulfuromonas, etc.) participate in the carbon and nitrogen cycles, and in the biogeochemical cycle of other elements. In short, Jerusalem artichoke can improve not only the physical and chemical properties of saline-alkali soil, but also promote material circulation and energy flow in the micro-ecological rhizosphere environment of saline soils.