Effective　disinfection　measures　are　in　urgent　need　due　to　the　serious　biosafety　issues　in　domestic　hot　water　supply　system.　In　this　study,　biofilms　annular　reactor　was　applied　to　simulate　the　domestic　hot　water　pipeline　system.　The　effects　of　chlorine　and　chlorine　dioxide　on　microbial　inactivation　in　biofilm　were　investigated.　The　changes　of　microbial　community　and　the　surface　structure　of　biofilm　were　further　explored　using　Illumina　MiSeq　sequencing　and　scanning　electron　microscopy　(SEM).　The　results　show　that　by　increasing　disinfectant　concentration,　the　microbial　inactivation　rate　could　be　notably　improved　while　the　inactivation　effect　remained　stable.　1.5　mg/L　chlorine　or　chlorine　dioxide　did　not　achieve　a　good　microbial　inactivation　effect.　However,　the　complete　inactivation　of　Escherichia　coli,　total　number　of　bacteria　and　heterotrophic　bacteria　(HPC)　were　observed　in　the　presence　of　3-5　mg/L　chlorine　and　chlorine　dioxide.　3-5　mg/L　chlorine　and　chlorine　dioxide　can　effectively　control　the　biofilm　of　hot　water　pipeline.　The　results　suggest　that　adequate　concentration　of　disinfectant　and　disinfection　time　are　important　for　keeping　high　inactivation　effect.　The　pipeline　biofilm　was　high　in　bio-diversity.　Different　from　those　in　municipal　water　supply　system　and　the　secondary　water　supply　system,　the　predominant　phyla　of　pipeline　biofilm　were　Deinococcus-Thermus　and　Proteobacteria,　as　well　as　some　detected　pathogenic　bacteria.　The　shock　disinfection　of　chlorine　or　chlorine　dioxide　showed　a　different　inactivation　effect　on　each　phylum.　Specifically,　compared　with　chlorine,　chlorine　dioxide　had　a　better　inactivation　effect　on　pathogenic　bacteria,　Proteobacteria,　and　Chlamydiae.　The　results　of　SEM　indicate　that　the　surface　structure　of　biofilm　was　effectively　destroyed　by　chlorine　and　chlorine　dioxide,　resulting　in　the　larger　gaps,　shrinkage,　and　shedding　of　biofilm.　Moreover,　the　effect　of　chlorine　dioxide　on　biofilm　surface　structure　was　higher　than　chlorine.　Overall,　the　results　are　important　for　the　biosafety　in　hot　water　system.　©　2019,　Editorial　Board　of　Journal　of　Harbin　Institute　of　Technology.　All　right　reserved.