The Yarlung Tsangpo River is the largest river in Tibet, China. Due to the increasing anthropogenic disturbance and ongoing development of water resources in recent years, there is an urgency to conduct a comprehensive investigation and evaluation for its aquatic biodiversity. Based on extensive ichthyological surveys across the whole basin of the Yarlung Tsangpo River, this study analyzed the fish diversity by integrating 12 indices of three dimensions, i.e., species diversity, functional diversity and phylogenetic diversity. Our results showed that a total of 37 fish species were collected from 24 sampling sites, belonging to 3 orders, 7 families and 24 genera. There were 27 species of native fish and 10 species of exotic fish. Among them, Cyprinidae was the dominant group. A hierarchical clustering based on species abundance data indicated that fish communities from different sampling sites could be divided into four groups. The dissimilarities occurred between the upper and lower reaches of the estuary of the Parlung Tsangpo River and between the mainstem and tributaries within both sections, which was highly related to regional biogeographical history and river environmental gradient. Twelve indices were applied to evaluate fish biodiversity for different groups. Except for Simpson richness index, Pielou evenness index, mean pairwise phylogenetic distance index and mean nearest phylogenetic distance (MNTD) index, significant differences were detected in other 8 indices among four groups. The correlation relationships among 12 diversity indices were different. Most of the indices related to species richness showed significant or extremely-significant positive correlations with each other. Functional divergence index and MNTD index showed significant or extremely-significant negative correlations with most of other indices, demonstrating the unique value of those indices from different categories. Based on the examination results of community functional-trait structure and phylogenetic structure, fish community assembly was supposed to be driven by competitive exclusion at most sampling sites, which was supposed to be related to the intense interspecific nutritional competition caused by poor nutrition and scarce food sources in the Yarlung Tsangpo River. In this study, multi-faceted diversity indices were used to explore the fish diversity and community assembly process in the Yarlung Tsangpo River, which can thus provide scientific basis for conservation and management of fish resources in this drainage as well as offer reference for future study on evaluating freshwater fish diversity.