In order to comprehensively evaluate the application effects of in-situ and ex-situ biofloc technology for shrimp culture, growth performance, parameters of shrimp serum physiological, biochemical, and immunological of shrimp cultured in in-situ biofloc (IB) and ex-situ biofloc (EB) systems were investigated. A load of Vibrios in the water body and hepatopancreas of shrimp, concentrations of NH4+-N and NO2--N in aquaculture water, as well as the bacterial community composition in flocs in IB and EB systems were monitored. The results indicated that the weight gain and specific growth rates of shrimp in group IB were significantly higher than those in group EB, feed conversion ratio in group IB was lower than that in group EB. Analysis of physiological and biochemical indicators showed that the activity of serum glutathione peroxidase (GSH-Px) in IB was significantly higher than that in EB (P<0.05). Conversely, the total antioxidant capacity (T-AOC) in IB was lower than that in the EB (P<0.05), content of total cholesterol (T-CHO), total protein (TP), albumin (ALB), activities of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) showed no significant differences between group IB and EB(P>0.05). Activity of phenoloxidase (PO) in shrimp of group IB was higher than that in EB (P<0.05). However, the activities of peroxidase (POD), catalase (CAT), superoxide dismutase (SOD), and lysozyme (LZ) showed no significant differences between group IB and EB(P>0.05). Vibrios load in water of group IB was significantly lower than that in group EB (P<0.05), However, the difference in Vibrios load in shrimp between group IB and EB was not statistically significant (P>0.05). Concentration of NO2--N and NH4+-N in group IB were significantly lower than those in group EB, respectively, at all sampling times (P < 0.05), except for no significant difference of NH4+-N between IB and EB on day 50. Moreover, the bacterial diversity of group IB was significantly higher than that of the EB. Taken together, in-situ bioflocs demonstrated superior performance over ex-situ bioflocs in promoting shrimp growth, improving water quality, and reducing Vibrio density. These findings could provide theoretical support for the wider application of biofloc technology in shrimp aquaculture systems.