In this study, we added Bacillus licheniformis to the diet of hybrid sturgeon (Acipenser baerii ♀ Acipenser schrenkii ♂) to determine its effects on growth performance, blood physical and chemical indices and intestinal microflora composition. One hundred and sixty adult hybrid sturgeon were selected and fed with four types of diets (equal nitrogen and fat levels) that were respectively supplemented with 0.00% (control group), 0.10% (Group B), 0.20% (Group C) and 0.40% (Group D) B. licheniformis for 120 days. Results showed that the fish in group C had the highest final body weight, weight gain rate and specific growth rate (p < 0.05). The feed coefficients, crude protein and crude fat of group B, group C and group D were significantly lower than that of group A (p < 0.05). And the crude protein (CP) and crude fat (EE) in groups B, C and D were significantly higher than the control group (p < 0.05). The serum TC and TG, ALP, ALT, AST and GLU contents in the B. licheniformis-added groups were also significantly higher than those of the control group (p < 0.05). In addition, Cetobacterium was the dominant bacterial taxon in each group. With increasing the content of B. licheniformis in the diet, the Cetobacterium content decreased and the Plesiomonas content increased correspondingly. Adding B. licheniformis to the diet greatly decreased the abundance of Streptococcus, Candidatus Competibacter and Lactococcus. Our results indicated that appropriately adding (0.20%) B. licheniformis could increase growth, reduce the feed coefficient and increase the diversity of the intestinal microbiota of hybrid sturgeon.