To elucidate the mechanisms underlying tolerance to saline-alkaline stress in two rice genotypes, Dongdao-4 and Jigeng-88, we exposed them to medium supplemented with 10 mM Na₂CO₃ and 40 mM NaCl (pH 8.5). Dongdao-4 plants displayed higher biomass, chlorophyll content, and photosynthetic rates, and a larger root system than Jigeng-88 under saline-alkaline conditions. Dongdao-4 had a higher shoot Na⁺/K⁺ ratio than Jigeng-88 under both control and saline-alkaline conditions. Dongdao-4 exhibited stronger rhizospheric acidification than Jigeng-88 under saline-alkaline conditions, resulting from greater up-regulation of H⁺-ATPases at the transcriptional level. Moreover, Fe concentrations in shoots and roots of Dongdao-4 were higher than those in Jigeng-88, and a higher rate of phytosiderophore exudation was detected in Dongdao-4versus Jigeng-88 under saline-alkaline conditions. The Fe-deficiency-responsive genes OsIRO2, OsIRT1, OsNAS1, OsNAS2, OsYSL2, andOsYSL15 were more strongly up-regulated in Dongdao-4 than Jigeng-88 plants in saline-alkaline medium, implying greater tolerance of Dongdao-4 plants to Fe deficiency. To test this hypothesis, we compared the effects of Fe deficiency on the two genotypes, and found that Dongdao-4 was more tolerant to Fe deficiency. Exposure to Fe-deficient medium led to greater rhizospheric acidification and phytosiderophore exudation in Dongdao-4 than Jigeng-88 plants. Expression levels of OsIRO2, OsIRT1,OsNAS1, OsNAS2, OsYSL2, and OsYSL15 were higher in Dongdao-4 than Jigeng-88 plants under Fe-deficient conditions. These results demonstrate that a highly efficient Fe acquisition system together with a large root system may underpin the greater tolerance of Dongdao-4 plants to saline-alkaline stress.