Phytoremediation efficiency can be enhanced by regulating rhizosphere processes, and the Cd isotope is a useful approach for deciphering Cd transport processes in soil–plant systems. However, the effects of adsorption and complexation on Cd isotope fractionation during the rhizosphere processes remain unclear. Here, we cultivated the Cd hyperaccumulator Sedum alfredii and Cd-tolerance Sedum spectabile in three different soils with citric acid applied as a degradable rhizosphere biostimulant. Cellular elemental distributions in the tissues and Cd isotope compositions were determined through NanoSIMS and MC-ICP-MS, respectively. Cd precipitation/adsorption on cell walls and intracellular regional distribution were the main mechanisms of Cd tolerance in S. spectabile. Plant roots became enriched with heavier Cd isotopes relative to the surrounding soils upon increasing secretion of rhizosphere organic acids. This indicates that organic matter with O and N functional groups preferentially chelates heavy Cd isotopes. In addition, Cd isotope fractionation between roots and shoots varies within the three soils, which could be due to the influence of protein and metallothionein contents in roots and leaves. The finding indicates that sulfur-containing ligands preferentially chelate light Cd isotopes. This study suggests that organic ligands play a vital role in Cd isotope fractionation and consequent hyperaccumulation of soil–plant systems.