The aim of our study was to unveil the promoting function of compound Bacillus sp. in improving chicken digestion-induced higher body growth performance. Strains of Bacillus subtilis and B. licheniformis were jointly supplemented to the chick diet. Digestive enzyme activities in the digesta improved, development of intestinal villus enhanced, and duodenum and ileum villous height increased, while their crypt depth declined, and the cecum’s bacterial composition optimized after 56 days of supplementation. Bacterial composition at the phylum level changed significantly, more Firmicutes, Proteobacteria, Epsilonbacteraeota, and Tenericutes, but fewer Bacteroidetes were detected in cecum digesta in the compound Bacillus supplemented group. Bacterial composition diversity, which improves the abundances of metabolic genes through KEGG pathway classification, became more abundant. Results indicated that the Ruminococcaceae UCG-005, unclassified Ruminococcaceae, and unclassified Lachnospiraceae species are actively correlated with body growth, promoting higher final body weight. In conclusion, owing to digestive enzyme secretion, the development of intestinal villus was stimulated and gastrointestinal bacterial composition optimized, and two combined Bacillus sp. improved chicken body growth. Our findings show the promoting action of Bacillus subtilis and B. licheniformis on digestion, which can be an alternative to antibiotics.