Sequential flooding and draining substantially alter Cd mobilization in paddy fields, primarily due to redox-driven changes in Fe-Mn (hydro)oxides and Cd-sulfides. However, the impacts of carbonates on Cd mobilization during flooding-drainage alternations remain poorly understood. In this study, Cd isotope compositions were analyzed in soils and plants at three growth stages, and the results show a pH-dependent Cd mobilization and isotope fractionation. Sequential extraction shows the Cd mainly binds to the exchangeable fraction and carbonates, and their amounts vary with pH. Exchangeable Cd with light isotopes coprecipitates into carbonates due to increased pH during flooding (tillering and panicle initiation). Whereas in drained soils (maturity), the carbonate-bound Cd releases with decreased pH. Light isotopes are enriched in rice compared with exchangeable Cd, but this enrichment is insignificant at maturity. This difference is mainly caused by the change in Cd isotope composition of exchangeable Cd pool due to carbonate coprecipitation during flooding. Limited isotope fractionation between roots and aboveground tissues is found at tillering, whereas significant isotope fractionation is observed at two other stages, suggesting the nodes might work during Cd translocation between tissues. These findings demonstrate alternating flooding-drainage impacts the mobilization of carbonate-bound Cd and, consequently, isotope fractionation in soil-rice systems.