Iron deficiency is the most common nutritional deficiency disorder in early postnatal period, which often manifesting into clinical complications. Therefore, iron supplementation is necessary to avoid iron deficiency anemia in the neonatal period. However, how to supplement iron effectively is a big problem. Thus, using newborn piglets as a model for iron deficiency, we compared the effects of routinely used protocol by intramuscular injection of high amount of iron dextran and a modified strategy by split iron supplementation with reduced amounts of iron. The results showed that split iron supplementation efficiently improved hematological status of piglets and attenuated the induction of hepcidin expression, which resulted in the recovery of piglets from iron deficiency and the increase of iron utilization. Compared with piglets received large amounts of iron dextran, low dose supplementation of iron improved the growth performance and duodenum development by increasing the villus height and crypt depth and enhancing microvilli morphology. Furthermore, split iron supplementation minimized the potential toxicity of the administered iron due to the oxidative stress and hepatocyte autophagy. Overall, the present study demonstrated that split supplementation with reduced amount of iron dextran not only protected newborn piglets from iron deficiency but also eliminated potential toxicity. It suggested that besides combating anemia, possible negative effects of excessive iron on oxidative stress, which is especially important for infant development, should be considered.