Organic iron is expected to replace inorganic iron used in diets as an iron source. Organic iron possesses high absorption efficiency and low fecal iron excretion. This study aims to study the effect of organic iron produced by Saccharomyces cerevisiae (yeast iron) on digestion, utilization, antioxidation and caecum microflora in weaned piglets. In total, 20 piglets that had been weaned after 28 days were divided into 4 groups, each of which followed a different basal diet. The basal diet of each of these 4 groups contained, respectively, 104 mg/kg iron (ferrous sulfate, CON), 84 mg/kg iron (yeast iron, LSC), 104 mg/kg iron (yeast iron, MSC) or 124 mg/kg iron (yeast iron, HSC). This experiment lasted 35 d. The apparent digestibility of iron in LSC, MSC and HMS was higher than that in CON (p < 0.01) and the fecal iron content in LSC, MSC and HMS was lower than that in CON (p < 0.01). Serum iron contents in LSC, MSC and HMS were higher than that in CON (p < 0.01). The iron contents of the heart, lungs, liver, kidney and left gluteus muscle in the MSC and HMS groups were higher than that in CON and LSC (p < 0.05). Serum catalase, glutathione peroxidase, superoxide dismutase activity, superoxide anion, glutathione, hydroxyl free radical scavenging rate, total antioxidant capacity, and liver superoxide anion clearance rate and peroxidase in MSC and HMS were higher than that in CON and LSC (p < 0.05). The contents of nitric oxide and peroxide of the weaned piglets in MSC and HMS were lower than that in CON and LSC (p < 0.05). The abundance of Firmicutes, Blautia and Peptococcus in LSC, HSC and MSC was higher than that in CON (p < 0.01). The abundance of Lactobacillus in CON and LSC was higher than that in MSC and HSC (p < 0.01). The abundance of Acinetobacter, Streptococcus and Prevotella in LSC, MSC and HSC was lower than that in CON (p < 0.01). The results suggested that a diet containing 84 mg/kg iron of yeast iron has the same effect as a diet containing 104 mg/kg iron of ferric sulfate, and that a diet containing 104 or 124 mg/kg iron of yeast iron is superior to a diet containing 104 mg/kg iron of ferric sulfate.