In spite of various advantages of biofloc technology in aquaculture, few studies have focused on the health status of fish in biofloc system. In this survey, the effect of cane molasses as a carbon source of biofloc system on hemato-immunological parameters, antioxidant status, and stress indicators of common carp (Cyprinus carpio) was investigated. Four hundred and twenty juvenile common carp (40.2 ± 5.76 g) were randomly divided into four equal groups in triplicates as follows: groups A, B, and C were reared in biofloc system with molasses as a carbon source with C/N ratio of 15, 20, and 25, respectively, whereas control group (D) was reared in similar intensity without biofloc system. Fish were reared for 90 days and samples were taken on days 0, 30, 60, and 90 of the experiment. Immunological parameters including serum lysozyme and bactericidal activity, serum complement and IgM level, and NBT reduction and resistance to bacterial challenge as well as hematological parameters (RBC, WBC, hematocrit, hemoglobin) were assessed in experimental groups. Meanwhile, antioxidative enzyme activity (glutathione and superoxide dismutase, catalase) and stress indicators (glucose and cortisol level) were measured and compared among the groups. Water quality parameters were evaluated in all groups. Results showed that most of the immunological parameters as well as resistance against bacterial infection increased in biofloc groups (particularly in C/N = 20 groups) (P < 0.05). Hematological parameters and antioxidative enzyme activity were not affected by biofloc systems. Stress indicators showed a significant decrease in biofloc system, particularly in C/N = 20 group compared with control (P < 0.05). The results indicated that biofloc system (particularly C/N ratio = 20 groups) could not only improve immunological parameters, antioxidative status, and water quality but it decreased stress statues of common carp.