Human pathogenic bacteria (HPB) are widespread in municipal wastewater and pose a serious threat to human health. In this study, we used a wastewater treatment plant in Nanjing as an example. The water samples of influent, sludge and biochemically treated effluent were collected monthly in a year. The composition of HPB community was characterized by PCR amplification targeting 16S rRNA gene and highthroughput sequencing, and the correlation between water physicochemical indexes and the composition of HPB community during biochemical treatment was investigated. The results showed that the number of detections and total relative abundance of HPB in the influent and biochemically treated effluent were relatively stable; the number of detections of HPB in sludge was more variable, and the total relative abundance was generally higher than that in the influent and the effluent, and showed obvious seasonal varieties. The composition of HPB in the influent, sludge, and effluent samples were similar, and the dominant HPB included Shigella boydii,Salmonella enterica,Pseudomonas aeruginosa, Mycobacterium tuberculosis,Enterococcus faecalis and Acinetobacter baumannii.Among the water physicochemical indexes, BOD₅,NO^-₃-N, TN were significantly correlated with the composition of the HPB community in the biochemically treated effluent. The relative abundance of Enterococcus faecalis was significantly positively correlated with BOD₅ concentration and negatively correlated with NO^-₃-N and TN concentration; the relative abundance of Shigella boydii was significantly positively correlated with NO^-₃-N and TN concentration and negatively correlated with BOD₅concentration.