Coreius guichenoti is an endemic fish in the upper reaches of the Yangtze River. It is of great significance to study the population viability changes of C. guichenoti under the construction of cascade hydropower stations in the Jinsha River for the protection of this species. The Vortex model improved conventional population assessment methods by incorporating factors like population age structure, reproductive system, sex ratio, and the impact of randomness on populations, such as environmental factors, disasters, population dynamics, and heredity. The model effectively simulates population responses to environmental changes, long-term patterns, and the principles governing fluctuations in population size. It is a widely used model for population viability analysis. This research based on resource survey data of the Jinsha River from 1981 to 2021. The Vortex model was used to construct the population dynamic model of C. guichenoti before and after the large-scale hydropower development in the main stream of the middle and lower reaches of the Jinsha River. The model considered the impacts of changes in water temperature and velocity environmental factors caused by hydropower development on population characteristics, and compared the population quantities, structures, and viabilities of C. guichenoti between these two periods. The results showed that before hydropower development, overfishing posed a significant threat to the population. Meanwhile, the population quantity decreased by 12.5% in 10 years, and the intrinsic growth rate was 0.085 in 100 years. The population viability was relatively stable, and the extinction probability was 1%. After hydropower development, the population quantity declined by 42% in 10 years, the intrinsic growth rate decreased to -0.087, and the extinction probability increased to 36.1%. The average extinction time of C. guichenoti was 83.7 years. The viability of C. guichenoti to resist environmental disturbance decreased. The population viability was affected.