To assess the impact of cascade hydropower stations on the health of aquatic ecosystem in the middle reaches of Jinsha River and to explore and establish relevant evaluation systems， surveys of fish resources and water environmental elements were conducted in December 2021， April 2022， and July 2022 in both the reservoir and tailwater parts of each station and its primary tributaries. Historical survey data from April to May 2007， March to April 2008， and June to July 2008 were utilized as reference conditions. The distribution range， discriminant capacity， and redundancy of the selected indicators were sequentially performed. Evaluation criteria were established through the implementation of the ratio method. Consequently， specific fish-index of biotic integrity （F-IBI） assessment frameworks tailored to both the main stem and tributaries of the Jinsha River were formulated. Additionally， an investigation into the correlation between F-IBI scores and various water environmental factors was undertaken. The results suggested that： Evenness index （M3）， percentage of cyprinid species （M4）， percentage of mid-lower layer fish species （M11）， percentage of individuals of fish producing floating eggs （M18）， and total number of fish individuals （M22） were screened out and analyzed as main stem core indicators. While percentage of loach species（M5）， M11， percentage of carnivorous fish individuals （M13）， M18， percentage of individuals with special spawning methods （M21） and M22 were filtered as tributaries core indicators. 32 monitoring points have been set up in the middle reaches of the Jinsha River. F-IBI scores range from 6.54 to 63.11 points， with evaluation grades of “sub-healthy”， “normal”， “medium risk”， “high risk” and “fishless” accounting for 3.70%， 29.6%， 48.1%， 11.1%， and 7.4% of monitoring points， respectively. In terms of correlations， the F-IBI values demonstrated a significant negative association with water temperature （WT， r=-0.404 9， P=0.044 7） and a significant positive correlation with secchidepth（SD， r=0.569 1， P=0.003 0） and flow velocity （v， r=0.450 9， P=0.046）. In conclusion， the research results indicated that the cascade hydropower stations in the middle reaches of the Jinsha River exerted a significant impact on the overall health of its aquatic ecosystem， with a notably higher level of impact observed in the tributaries compared to the main stem.