To investigate the influence of pipe materials on species of pathogens in water distribution system, a drinking water distribution system (DWDS) in a city in eastern China which has been operating steadily for eight years was taken as the experimental object. Metagenomic sequencing analysis was conducted to study the effects of pipeline materials on pathogens in 13 sets of biofilms collected from ductile iron pipe (DCIP), polyethylene pipe (HDPE), galvanized steel pipe (GSP), stainless steel composite pipe (SSCP), and steel pipe (SP). Results show that the relative abundance of pathogens in DCIP biofilm was the most, while that in GSP biofilm was the least. In addition, nine of 12 pathogens on the global priority pathogens list published by WHO were detected from the water distribution pipeline, with relative abundance ranged from 0.079% to 1.084%, indicating the severe hazard potential of biofilms in water supply pipelines to humans and the environment. Based on the relative abundance distributions of the pathogens in five pipe materials, the priority pathogens associated with the five pipe materials were found. The research results provide an effective and theoretical basis for the selection of water distribution pipe materials.