The importance of Bacillus as feed additives in animals’ production is well recognized. Bacillus amyloliquefaciens and Bacillus pumilus are involved in promoting animal growth performance and immunological indicators. However, their precise roles in the modulation of microbiota and immune response in goat rumen and intestines have not been investigated. The aim of the current work was to evaluate the impacts of Bacillus amyloliquefaciens fsznc-06 and Bacillus pumilus fsznc-09 in the development of rumen and small intestinal and microbial communities in rumen and caecum of weanling Jintang black goats. Morphological alterations of rumen and small intestine (duodenum, jejunum, and ileum) were evaluated by histochemical staining, and ruminal contents and cecal feces were analyzed by 16S rRNA sequencing in an Illumina NovaSeq platform. Morphological analysis showed that feeding weanling goats with Bacillus amyloliquefaciens fsznc-06 or Bacillus pumilus fsznc-09 enhanced ruminal papilla and small intestinal villus growth. In addition, 16S rRNA sequencing analysis indicated that microbial richness and diversity (Shannon, Simpson, Chao1, and ACE) and the relative richness of multiple or potential beneficial bacteria were higher in weaned black goats fed on Bacillus amyloliquefaciens fsznc-06 or Bacillus pumilus fsznc-09, but that of multiple or potentially pathogenic bacteria were lower, as compared with the control group. Tax4Fun analysis predicting the functional profiling of microbial communities showed that microbial communities in rumen or caecum were highly influential on metabolism and organism systems after feeding weanling goats with Bacillus amyloliquefaciens fsznc-06 or Bacillus pumilus fsznc-09. It was suggested that Bacillus amyloliquefaciens fsznc-06 and Bacillus pumilus fsznc-09 might be an auspicious antibiotic alternative to improve black goat growth and health by changing rumen and gut microbiota positively.