The gut microbiome plays important roles in the regulation of gastrointestinal tract functional development and host mucosal immune maturation. This study was conducted to test the hypothesis that age and feeding system (supplemental feeding [Sup] vs. grazing [G]) could alter colonic bacterial diversity and host mucosal immune maturation. Thirty Liuyang black goat kids ( = 4) were slaughtered on d 0, d 7 (nonrumination), d 28, d 42 (transition), and d 70 (rumination). The colonic microbiota was profiled by Miseq sequencing of the 16S rRNA gene. Host colonic mucosal immune maturation was examined using mRNA level expression of Toll-like receptors (TLR), proinflammatory cytokines, and the Toll-IL-1R (TIR) domain-containing adaptor. A correlation analysis was conducted to elucidate the relationship between bacterial diversity and fermentation parameters and host immune maturation variables. The results showed that α diversity indexes ( < 0.05), abundances of genera ( = 0.003) and ( = 0.024), ( = 0.004), and ( = 0.046) mRNA expressions were lower for Sup than for G, whereas the abundance of genera and ( < 0.05) was greater for Sup than for G. Regardless of the feeding system, bacterial 16S rRNA gene copy number and α diversity indexes increased ( < 0.05), whereas Proteobacteria abundance decreased linearly from d 0 to 70 after birth ( = 0.026). At the genus level, dominated the first week and declined sharply afterward, whereas abundance was greatest on d 7. abundance decreased linearly ( = 0.021), whereas abundances of , , , , and increased with age ( < 0.05). These findings coincided with increased , , and myeloid differentiation factor 88 () mRNA expressions with age ( < 0.05). Finally, correlation analysis revealed that different genera participated in different roles in fermentation capacity and host mucosal immune maturation. Collectively, colonic bacterial diversity and host mucosal immune maturation are age related, and concentrate supplement could alter bacterial diversity and alleviate overinflammation responses.