This study investigated the effects of replacing fish meal (FM) with biofloc meal (BM) on the growth, digestion function, protein metabolism, lipid metabolism, immunity, antioxidant capacity and intestinal microbiota of common carp (Cyprinus carpio). The experiment includes two trials (a growth trial and a digestibility trial). In the growth trial, the control diet contained 20% FM. And five isonitrogenous and isolipidic diets were formulated to replace 0% (CK), 20% (BM20), 40% (BM40), 60% (BM60) and 80% (BM80) of the FM protein with BM. The five diets were fed to common carp (3.73 ± 0.01 g) for 56 days. The results indicated that the growth performance [final weight (FW), specific growth rate (SGR) and feed efficiency ratio (FER)] and digestive enzymes activities displayed a noteworthy quadratic trend with the increasing replacement level of FM with BM (P < 0.05), reaching a maximum at the BM40 group and a minimum at the BM80 group. Regression analysis of weight gain rate (WGR) against the substitution level found that the optimal level of BM replacing FM was 34.12%. The appropriate levels of BM could improve protein metabolism and lipid metabolism by regulating the expressions of related genes. Regarding the expression levels of PI3K, mTOR and HSL mRNA, they were the highest in the BM40 group and the lowest in the BM80 group, while the levels of ACC and FAS mRNA were reversed (P < 0.05). Simultaneously, the number of lipid vacuoles in the BM80 group were significantly increased than the CK group. Replacing 40% FM with BM augmented the fish immunity and antioxidant capacity, as showed by elevated the C3, C4 and IgM levels as well as CAT and SOD activities, and reduced the expression levels of NF-κB, TNF-α and Keap1 (P < 0.05). Regarding intestinal microbiota, replacing 40% FM with BM could improve the intestinal microbiota structure. The digestibility trial results showed that the apparent digestibility of protein and lipid in BM of common carp was slightly lower than FM. Conclusively, replacing 40% FM with BM could promote growth, immunity and protein metabolism of common carp, but excessive substitution level (80%) could compromise growth and hepatopancreas health.