In order to study the effects of Bacillus subtilis HGcc-1 on the gut and liver health, serum complement and gut microbiota of Cyprinus carpio fingerlings, healthy C. carpio fingerlings with a body weight of (13.10±0.39) g were selected, and randomly divided into HGcc-1 supplementation group and control group, and after 20 weeks of feeding, the growth indicators were measured, and the C. carpio serum endotoxin (LPS), Alanine aminotransferase (ALT), Aspartate aminotransferase (AST), total complement and lysozyme were detected, and 16S rRNA sequencing of the gut microbiota was made. At the same time, the gut microbiota induced by HGcc-1 supplement group and the control group were transferred to germ free Danio rerio, and then the levels of endotoxin binding protein (LBP), ALT and AST and the expression levels of C3 and C4 genes of germ free D. rerio were measured; finally, the levels of ALT and AST and the expression levels of C3 and C4 genes in germ free D. rerio were tested when HGcc-1 directly acted on germ free D. rerio. The results showed that HGcc-1 had no effect on the weight gain rate of C. carpio, but adding HGcc-1 significantly reduced the level of serum endotoxin, ALT and AST. The serum total complement level of the HGcc-1 supplement group was significantly increased, compared with control group. The 16S rRNA sequencing results showed that at the phylum level, the HGcc-1 supplement diet group increased the abundance of Fusobacterium by 47.1% compared to control group; the abundance of Proteobacteria was decreased by 70.7% compared with the control group; at the genus level, the HGcc-1 supplement diet group increased the abundance of Cetobacterium by 47.1% compared with the control group; the abundances of Citrobacter and Aeromonas were reduced by 56.6% and 70.9% respectively, compared with the control group. And it was further observed that the intestinal microbiota of HGcc-1 addition group decreased the content of endotoxin binding protein (LBP) and level of AST of the germ free (GF) D. rerio, and significantly increased the gene expression of complement component 3 and the complement component 4 (C3 and C4) of the GF D. rerio. At the same time, the direct interaction between HGcc-1 and GF D. rerio also decreased the ALT and AST levels of the GF D. rerio. This study shows that dietary B. subtilis HGcc-1 can improve the gut and liver health, serum complement and intestinal microbiota homeostasis of C. carpio fingerlings. This study laid a theoretical foundation for the further application of B. subtilis HGcc-1.