Scope: Iron deficiency anemia (IDA) in children is one of the most common nutrition-related health conditions worldwide. Prebiotic oligosaccharides, fructo-oligosaccharide (FOS) and galacto-oligosaccharides (GOS), have shown to affect iron absorption in anemic subjects, but the results in previous studies are inconsistent, thus the underlying mechanism and the effective dose of GOS in mitigating anemia remain unclear. Methods and Results: The present study aims to investigate the mechanism of how GOS/FOS affect iron absorption in an iron-deficient growing rat model from the perspectives of protein expression and gut microbiota, and determine the optimum dose of GOS. Iron-deficient models are established by providing young rats diet without iron addition for 14 days. Later, iron-deficient rats are provided with standard rat chows supplemented with 0%, 3%, 5%, 10% GOS, and 10% FOS for 21 days. The results show that ≥5% GOS supplementation in diet improves iron status and significantly impacts iron-binding/transport protein expression. Furthermore, a dose-dependent modulating effect of GOS on gut microbiota is determined. Conclusion: For the first time, the present study provides evidence that GOS supplementation induces a dose-response effect on iron absorption and gut microbiota in the established model, suggesting a positive role of GOS in ameliorating IDA in children.