This study is aimed at exploring the effects of Bacillus coagulans NRS 609 on the growth performance, intestinal health, antioxidant activity, and immune response in common carp (Cyprinus carpio L.) by colonizing the intestinal tract with the beneficial strain. Gavage B. coagulans with GFP-tag at 109 CFU/mL into common carp for 7 days. Results indicated that B. coagulans were maintained in the intestine for at least 14 days. Four groups fed B. coagulans at different levels of inclusion, including 0 (CK),
1
×
10
7
(A),
1
×
10
8
(B), and
1
×
10
9
(C) CFU/g of feed for 8 weeks. Experimental groups showed significantly better growth performance than the control (
P
<
0.05
). The treatment groups had higher digestive enzyme activity, villus height, and muscle thickness than the control (
P
<
0.05
). Supplementation with B. coagulans also altered the composition of the intestinal flora. In addition, an enhancement of the antioxidant enzyme and a reduction of malondialdehyde in the liver were observed with the addition of B. coagulans (
P
<
0.05
). Moreover, the cytokines of IL-1β and IL-12, IL-10, and TGF-β, significant upregulation in experimental groups (
P
<
0.05
). Based on the results, the optimal level of B. coagulans was 107 CFU/g in diets for common carp.