Saline-alkali soils are globally widespread, and in the context of global climate change, soil salinization is worsening. Improving these soils is crucial for food security and soil carbon storage, and thus, various measures have been used to mitigate salinization. Iron oxides protect soil organic carbon (SOC) over the long term, but the effects of saline-alkali soil improvement on iron-bound organic carbon (Fe-OC) remain unclear. Using data from saline-alkali soil improvements in Northeast China, this study examined the effects of two improvement methods on Fe-OC: the application of one traditional amendment and one new type of amendment. Both significantly increased Fe-OC content, shifting its association from adsorption to co-precipitation, thereby enhancing the formation and stability of Fe-OC and consequently promoting SOC sequestration. Both also facilitated the transformation of free iron minerals into complexed forms, reducing microbial carbon binding while maintaining the pattern of preferential binding of iron minerals with aromatic-C. Key factors driving these changes include improved soil nutrients, water content, and microorganisms, along with reduced soil pH. The mechanism suggests that our findings hold broad significance, as irrespective of the type of saline-alkali soil or the specific improvement measures utilized, all effective saline-alkali soil improvement methods will ultimately lead to increased soil nutrients, water content, and microbial diversity, alongside a decrease in soil pH. These processes collectively facilitate the formation and stabilization of Fe-OC. This study offers new insights into the effects of saline-alkali improvements on Fe-OC and SOC stabilization.