Host-derived probiotics are widely used in aquaculture because they are able to adapt to the host intestinal environment more easily than other probiotics. However, decreased numbers and activity of live probiotics that occur during processing, storage, transportation, and consumption hinders the increased use of probiotics. In this study, the ability of sodium gluconate to promote the growth of Bacillus velezensis R7-1003, isolated from the intestinal tract of the common carp, was evaluated in vivo. The actions of dietary supplementation with B. velezensis R7-1003 and/or sodium gluconate were investigated in the common carp with respect to growth, the morphology of the intestine, digestive and immune functions, and antioxidant capacity, as well as intestinal microbiota. The results revealed that the addition of 0.3 and 0.6% sodium gluconate to the diet increased B. velezensis R7-1003 growth in the intestinal tract of the common carp. Furthermore, 0.6% sodium gluconate exhibited better results than 0.3%. A diet with host-derived B. velezensis R7-1003 supplementation improved the growth performance of the fish. It also increased the length of the intestinal villi and tight junction gene expression levels, including claudin-2, occludin, and ZO-1. Host-derived B. velezensis R7-1003 supplementation enhanced the activities of protease, alpha-amylase, lipase, alkaline phosphatase, acid phosphatase, lysozyme, catalase, glutathione peroxidase, decreased the level of MDA, increased the level of the anti-inflammatory cytokine TGF-beta, and decreased the level of the pro-inflammatory cytokine TNF-alpha. Furthermore, B. velezensis R7-1003 increased the levels of several probiotics, including Lactobacillus and Lactococcus, and bacteria that produce short-chain fatty acids, including Faecalibacterium, Bacteroides, and Clostridium. The ratio of Firmicutes/Bacteroidetes was reduced in the intestine of the common carp. Importantly, this study indicated that the combination of B. velezensis R7-1003 and sodium gluconate provided additional beneficial effects to the common carp. Thus, this study demonstrated that sodium gluconate promoted B. velezensis R7-1003 growth, which increased the growth performance and intestinal health of the common carp. The results indicated that further study is warranted concerning the use of B. velezensis R7-1003 combined with sodium gluconate as a diet supplement in other economically viable fish.