Bacillus is one of the most common probiotics used in aquaculture. This study revealed the effects of different Bacillus species on the digestive enzyme activities, intestinal flora, and flesh quality of turbot. Moreover, this study also indicated the correlations between the digestive enzyme activities, flesh quality and intestinal flora of turbot. Based on the purpose of this study, 96 healthy turbots were randomly divided into four experimental groups. Fish were fed by basal diet as control group (T0) and the basal diet supplemented by Bacillus subtilis SMF1, B. licheniformis LMF1 and B. siamensis DL3 were treaded as treatment group (B1), treatment group (B2), and treatment group (B3), respectively. The results showed that dietary supplementation with Bacillus sp. improved protease and lipase activities, the contents of total protein and fat of proximate carcass, and regulated the intestinal flora. It also affected the contents of certain amino acids, such as sulfur amino acids (SAAs). However, the effects of the dietary supplementation with Bacillus sp. on the contents of fresh and total essential amino acids were not significant. The dietaries with B. licheniformis LMF1 and B. siamensis DL3 promoted the increasing of the relative abundance of bacteria, such as unidentified_Clostridiales, unidentified_Enterobacteriaceae, and Romboutsia in the intestine. The promotions were related to the metabolism of sulfur compounds, which resulting in different SAAs in turbot carcass. Moreover, the dietary with B. subtilis SMF1 increased the contents of polyunsaturated fatty acids (PFAs) and docosahexaenoic acid (DHA) in the carcass of turbots. As the results showed, B. subtilis SMF1 significantly increased the relative abundances of Mycoplasma and Chryseobacterium in intestines of fish. The effects of the dietary with B. subtilis SMF1were positively related to PFAs or DHA levels. Meanwhile, Bacillus improved the nutritional composition of turbot carcass by promoting the probiotics in turbot intestine, such as Acinetobacter, Ralstonia, Lactobacillus, and Bifidobacterium, and reducing the relative abundance of the bacteria, such as Vibrio and Bacteroides in turbot intestine.