Abstract: To evaluate the impact of human activities of the Heishui River, which could be a potential alternative habitat for the lower reaches of the Jinsha River. Based on data of fish resource yearly surveyed in 2016-2018, The population structure and biodiversity of fish resources in the lower reaches of Heishui River were analyzed. Index of biological integrity (IBI) based on fish to assess the river health was established in this study. Results showed that there were 9 dominant fish specie in the Heishui River, including Paracobitis varigatus(IRI=6 370), Schistura fasciolata (IRI=2 418), Schizothorax wangchiachii (IRI=1 285), Triplophysa anterodorsalis (IRI=788), Trilophysa bleekeri (IRI=715) and so on. High numbers of endemic species distincted in this area, and the fish fauna was dominated by West China and South China biota. Four major metric parameters (i.e. number of species, presence of cyprinid species, proportion of omnivores individuals and proportion of herbivores individuals) were assessed by applying the fish biotic integrity index (F-IBI).The results of stream condition assessment showed that the river’s health was mainly at the status of “poor”, the middle-lower reaches and estuary section were fairly good. The assessment was consistent with the actual situation of human disturbance including the sand extraction, small hydropower development and overfishing in this river drainage. Aiming at the protection of fish biodiversity and improvement of river healthy, several situ conservation ways had applied including artificial enhancement and releasing of endemic fish, control reasonable discharge flow, closed fishing, remove the Laomuhe Dam and ecological restoration of fish habitat in this river. Long-time monitoring and evaluation can verify the adaptive effect of restoration project.