When the salvaged cyanobacteria was dehydrated by centrifugation, the algae pulp filtrate produced. And there were a large number of algae cell sap, nitrogen, phosphorus, and algae toxin. If it is discharged into water directly, it would cause secondary pollution. The downward-flow biological aerated filter was used to treat the algae pulp filtrate, and the removal effect of COD, NH3-N, TN, TP and MC-LR was investigated. The result showed that the average removal rate of COD, NH3-N, TN, TP and MC-LR were 73.4%, 91.6%, 39.6%, 13.2% and 88.3% respectively under the condition that the hydraulic loading was for 0.40 m 3/(m 2·h). The COD and NH3-N meet standard A of the first class in “Discharge standard of pollutants for municipal wastewater treatment plant”(GB18918-2002), and the concentration of MC-LR is lower than the limit of “Standards for Drinking Water Quality”(GB 5749-2006). The microbial species in biological aerated filter was analyzed. The dominant bacteria were Lysinibacillus, aeromonas, bacillus, acinetobacter, achromobacter, bacillus, fusiformis, and pseudomonas respectively determined by constructing phylogenetic tree. The cyanobacteria toxin degradation bacterium of T1 which was put in biological aerated filter in start-up grew well and form certain advantages.