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 80^th 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