Abstract: To address ecological health on Nanjing Section of the Changjiang River, we sampled at10mainstream sections and21tributaries in Nanjing Section in the dry and wet seasons of2019.High-throughput sequencing was used to analyze the structural composition of benthic bacterial communities, by which the benthic bacteria-index of biological integrity(B-IBI) was established.The results showed that the ecological health on Nanjing Section of Changjiang River was better in the normal water season than that in the wet season, and it was superior in the mainstream than in the tributaries.Total nitrogen, ammonium, nitrate, and total organic carbon were negatively correlated with the B-IBI,while the Shannon, Margalef, and Evenness indices were positively correlated.The established evaluation system effectively indicated the water quality and habitat conditions of the Changjiang River.Hard revetments or riverbeds negatively affected bacterial community diversity in tributaries.It is suggested to strengthen the ecological restoration of rivers on the basis of ensuring flood prevention.