Understanding the role of Jerusalem artichoke grown in low fertility coastal saline soil in carbon sequestration is important for characterizing the relationship between soil use in agriculture production and carbon sequestration. In the present study, the mechanisms of photosynthesis and carbon distribution were studied in three saline soils with different salt contents (Xinyang 0.6–1.0 g salt/kg; Dafeng 1.5–2.4 g salt/kg; Shuntai 3.8–4.5 g salt/kg) by characterizing the biomass production, carbon storage, and carbon sequestration in the soil under Jerusalem artichoke. The biomass production and carbon storage during the growth cycle of Jerusalem artichoke were significantly higher in Dafeng than the other plots. The highest carbon sequestration was found in the Xinyang plot. The organic matter content in the rhizosphere soil was 28–44% higher than that in the non-rhizosphere soil. The soil organic carbon content in the rhizosphere soil was higher than that in the non-rhizosphere soil. High soil salinities decreased the carbon storage of Jerusalem artichoke. Carbon sequestration in soil decreased with the increase in soil salinity.