We aimed to explore the effects of two different doses of Zn on the fecal microbiota in pigeons and the correlation between these effects and intestinal immune status. Zn doses affected pigeon growth performance, and pigeons in the T60 (60 mg/kg Zn) and T90 (90 mg/kg Zn) groups exhibited higher villus height and crypt depth in duodenum and ileum compared to the control group, respectively. Supplementation with Zn increased the expression of the IL8, CD798, TJP and NKTR genes (p < 0.05), while enhancing serum immunoglobulin (Ig) G, IgM, and IgA concentrations compared to the control pigeons (p < 0.05). T60 treatment reduced relative Actinobacteriota abundance, while Lactobacillus spp. abundance was highest in the T90 group compared to the two other groups. The core functional genera significantly associated with immune indices in these pigeons were Rhodococcus erythropolis and Lactobacillus ponti. Our findings will help facilitate the application of dietary Zn intake in pig production.