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<i>Enterococcus faecium</i> (<i>E. faecium</i>) and <i>Bacillus subtilis</i> (<i>B. subtilis</i>) are widely used as probiotics to improve performance in animal production, but there have been few reports of their impacts on pigeon milk. In this study, twenty-four pairs of parental pigeons were randomly divided into four groups, with six replicates, and each pair feeding three squabs. The control group drank normal water. The <i>E. faecium</i> group, <i>B. subtilis</i> group, and mixed group drank water supplemented with 3 × 10⁶ CFU/mL <i>E. faecium</i>, 2 × 10⁷ CFU/mL <i>B. subtilis</i>, and a mixture of these two probiotics, respectively. The experiment lasted 19 days. The results demonstrated that the IgA and IgG levels were significantly higher in the milk of Group D pigeons than in the other groups. At the phylum level, <i>Fimicutes</i>, <i>Actinobacteria</i>, and <i>Bacteroidetes</i> were the three main phyla identified. At the genus level, <i>Lactobacillus</i>, <i>Bifidobacterium</i>, <i>Veillonella</i>, and <i>Enterococcus</i> were the four main genera identified. In conclusion, drinking water supplemented with <i>E. faecium</i> and <i>B. subtilis</i> could improve immunoglobulin levels in pigeon milk, and this could increase the ability of squabs to resist disease. <i>E. faecium</i> and <i>B. subtilis</i> could be used as probiotics in the pigeon industry.