[Background] The Yangtze River flows across the Plateau of Tibet, mountain valley and plain. Its main channel is as long as 6 300 km, and upstream segment of the Yangtze River is regarded as Yibin in Sichuan province and Yichang in Hubei province, with a distance of about 1 030 km, and middle-stream segment of the Yangtze River is regarded as Yichang to Hukou in Jiangxi Province, with a distance of about 955km. Fish species diversity is richest across the Yangtze River Basin, but fishery catches are rapidly decreasing due to habitat destruction, environmental pollution and excessive fishing in the past decades, and declining fish biodiversity poses risks for fishes resources. Therefore, a “10-year Fishing Ban” plan was launched from January 2021, which aims to recover the fish stocks and aquatic resources across the Yangtze River Basin, but lack of spatial and temporal measurement for fish diversity changes in the Yangtze River, and identification of the change-drove factors can provide data for protection and management of fish communities in the Yangtze River. [Aim] In order to explore the driving factors of fish diversity change in the middle and upper reaches of the Yangtze River, and measure the change degree of fish diversity in the Yangtze River. [Methods] The data from investigation and the retrieved literatures were used to analysis the diversity and structure of fish community in the Yangtze River, and compared α and β diversity changes of fish communities at species and phylogeny levels during historical and current periods. [Results] The results showed that 174 species, belonging to 92 genus, 22 families, and 9 orders were found in the main channel of Yangtze River to date. Compared to historical period, 47 native species, and 27 endemic species decreased, but 11 invasive species increased in current period. There is signaling difference in between the upper and middle community construction, and the upper’s diversity was higher than that in the middle. 43 species contributed to the diversity rates of community construction. All species and native species showed that the average taxonomic distinctness increased from history to current at the α level, but the taxonomic distinct diversity decreased, and loss of native species resulted in the decrease of community diversity. The βs?r values of the upper and middle communities showed significant changes at the β level, which was drove by βsne. The βsne.phy that changed from 0.054 to 0.085 was mainly contribution to the changes of βsor.phy between the upper and middle communities from 0.29 to 0.314 at phylogenetic β level. The βsor.phy for the native species did not change significantly, and acquisition of exotic invasive species gave rise of the changes in community taxonomic units, further to result in significantly change between communities at phylogenetic β level. [Conclusion] The results show that the loss of indigenous species and the invasion of alien species have changed the spatial and temporal patterns of fish communities in the Yangtze River main channel, revealing that human activities and habitat changes significantly affect the phylogenetic diversity of fish communities in the Yangtze River main channel, which is expected to provide theoretical support for ecological restoration in the Yangtze River and the evaluation of the effect of "ten-year fishing ban".