Salinity is one of the main environmental constraints in soil restricting plant growth and agricultural productivity; however, the utilization of salt-affected land brings substantial benefits. This study investigated an in situ remediation method that involved planting Jerusalem artichokes in naturally occurring saline-alkali soils with different salinities (g salt kg −1 soil), specifically, high salinity (H, >4.0), moderate salinity (M, 2.0–4.0) and low salinity (L, 1.0–2.0), in the coastal saline zone of southeast China. We compared these conditions with corresponding soil controls that were not planted. Soil pH and salinity were increased in bulk and unplanted control soils compared to rhizosphere soils. Neutral phosphatase and invertase showed a significant negative correlation with soil salinity, and there was a significant positive correlation between these two enzymes. While catalase activity decreased in the reverse order. The lowest calcite, muscovite and quartz contents as well as the highest chlorite and albite contents were found in the control soils. Planting Jerusalem artichoke also enhanced bacterial microbiota in saline-alkali soils. Bulk soil Operational Taxonomic Units (OTUs) numbers at high (H), moderate (M) and low (L) salinity were 4177, 5325 and 3672, respectively, and they were 1.27, 1.02 and 1.25 times lower than those in rhizosphere soil. This finding demonstrated that the Jerusalem artichoke played a significant role in enhancing soil microbial richness. In conclusion, Jerusalem artichoke could improve the physical and chemical properties of the soil by released root exudates into soil, increased the diversity and richness of soil microbial communities, and so on, so as to achieved the effect of improved the saline-alkali soil in coastal areas of Dafeng, Jiangsu Province, which provided scientific basis for elaborated the salt-tolerant characteristics of Jerusalem artichoke and improved the mechanism of coastal saline soil function.