We report a recycling bioresource involving harvesting of Microcystis aeruginosa using the bioflocculant (MBF-32) produced by Enterobacter aerogenes followed by the recovery of the harvested M. aeruginosa as the main substrate for the sustainable production of MBF-32 and biohydrogen. The experimental results indicate that the efficiency of bioflocculation exceeded 90% under optimal conditions. The harvested M. aeruginosa was further recycled as the main substrate for the supply of necessary elements. The highest yield (3.6±0.1g/L) of MBF-32 could be obtained from 20g/L of wet biomass of M. aeruginosa with an additional 20g/L of glucose as the extra carbon source. The highest yield of biohydrogen was 35mL of H2/g (dw) algal biomass, obtained from 20g/L of wet biomass of M. aeruginosa with an additional 10g/L of glycerol. Transcriptome analyses indicated that MBF-32 was mainly composed of polysaccharide and tyrosine/tryptophan proteins. Furthermore, NADH synthase and polysaccharide export-related genes were found to be up-regulated.