Focused　on　the　potential　threat　of　the　membrane　fouling　to　the　bio-safety　of　the　drinking　water　in　the　second　water　supply,　this　study　investigated　the　effect　of　shock　chlorine　and　chloramine　disinfection　on　the　total　Bacteria,　Escherichia　Coli　and　Heterotrophic　(HPC)　bacteria　as　well　as　the　structure　of　the　biofilm　in　the　BAR-simulated　secondary　water　supply　system.　The　results　showed　that　the　number　of　microbes　in　the　biofilm　reached　maximum　on　the　80th　day　and　soon　it　fluctuated　smoothly.　The　Firmicutes,　Proteobacteria　and　Bacteroidetes　were　predominant　bacteria　by　Metagenomic　approaches.　The　effect　of　chlorine　and　chloramine　disinfection　on　the　biofilm　was　related　to　the　concentration　of　the　disinfectant　as　well　as　the　concentration　and　time(CT).　At　the　same　CT　value,　higher　concentration　of　Chlorine　and　chloramine　had　more　effective　disinfection.　Comparison　and　analysis　found　that　in　low　concentrations,　compared　to　chloramine,　chlorine　is　more　effective　to　total　Bacteria　and　Escherichia　Coli,　while　less　effective　to　HPC.　However,　in　high　concentrations,　chlorine　and　chloramine　own　nearly　the　same　inactivated　effect.　When　the　concentration　of　chlorine　and　chloramine　was　3.0　mg/L　and　the　CT　value　was　300-400　mg·min/L,　the　inactivation　rate　of　total　Bacteria,　Escherichia　Coli　and　HPC　was　as　high　as　95%.　Scanning　Electron　Microscope(SEM)　images　of　biofilm　surface　plot　analysis　illustrated　that　the　structure　of　biofilm　was　damaged　seriously,　and　shock　chlorine　disinfection,　compared　to　chloramine,　possessed　less　impact　to　the　structure　and　reduction　degree　of　the　biofilm　and　was　hence　more　conducive　to　the　biofilm　control.　©　2017,　Editorial　Board　of　Journal　of　Harbin　Institute　of　Technology.　All　right　reserved.