This study evaluated the feasibility of domesticating the bioflocs with activated sludge as inoculum at high salinity. By using the gradually increase salinity from 0.2 to 4.0%, the study evaluated the effectiveness of bioflocs in sustaining the water quality of aquaculture, the biofloc morphology characteristics and microbial community structure of bioflocs in order to discover the influence of salinity. From the perspective of sustaining the water quality of bioflocs, the COD removal efficiency dropped sharply from 63.9% to 3.7%, the NO3−-N was maintained below 0.5 mg/L but the NH4+-N exceeded the safety threshold of aquaculture at the salinity of 2.5–4.0%. From the pespective of flocculation of flocs, the biofloc volume index and content were maintained at about 30 ml/g and 7 g/L, while the floc particle size (45–200 um) tended to increase cumulatively, showing good agglomeration, sedimentation and stability. From the pespective of floc microbial community structure, Arenibacter, Thauera, Paracoccus and Denitromonas became the dominant genera with relative abundances of 4.8–7.5%, 4.9–17.1%, 3.0–4.7% and 5.3–14.1% at 3.0–4.0% salinity, respectively, however, the relative abundance of Candidatus Competibacter rapidly decreased from 15.0% to 2.5% with the increasing salinity from 1.0% to 4.0%. Furthermore, Redundancy analysis (RDA) indicated that salinity was a key environmental factor affecting floc community, and Functional Annotation of Prokaryotic Taxa (FAPROTAX) confirmed the promoted flocs denitrification as well as inhibited nitrification and hydrocarbon cycling in higher salinity to some extent. This study demonstrated the feasibility of using freshwater activated sludge as a base nucleus for biofloc formation for salinity up to 2% – 2.5%, which provided a useful reference for improving the taste and nutritional value of fish cultured by Biofloc Technology (BFT).