Periphyton algae are one of the main groups of organisms in the aquatic ecosystem. They are self-sustaining and can store solar energy by converting it into chemical energy through photosynthesis, as well as generate and release oxygen to promote the material circulation, energy flow and information transfer of the aquatic ecosystem. Periphyton algae are rich in species, attached growth, short life cycle, sensitive to changes in the water environment, and can absorb pollutants in water bodies and purify water quality. They are the beginning of the food chain in the water ecosystem and an important indicator species for water quality monitoring, and often used to the health evaluation of aquatic ecosystems. The Yarlung Zangbo River Basin has high average altitude, low water temperature, and strong ultraviolet radiation, which is the most important natural aquatic ecosystem in Tibet Autonomous Region. It can adjust the climate characteristics of Tibet Autonomous Region and has special geomorphological and ecological conditions that many low altitude rivers do not have, the ecological environment is very sensitive and fragile, and it is highly susceptible to events such as global climate change and human disturbance. Ensuring its water environment has a high health status is an important foundation for protecting green mountains and rivers. In order to assess the health status of the water ecosystem, 26 sampling points were set up on the main stream and four major tributaries of the Yarlung Zangbo River Basin from 2013 to 2014. The environmental data and the periphyton algae community were collected, and the periphytic index of biological integrity (P-IBI) were constructed. A total of 7 phyla, 10 classes, 23 orders, 34 families and 70 genera (species) of periphyton were identified, most of which were Bacillariophyta (35.71%), Chlorophyta (32.86%) and Cyanophyta (20.00%), and the dominant species of periphyton algae were the Bacillariophyta belonging to Bacillariophyta-chlorophyta-cyanophyta type of water. The species richness and total abundance of periphyton algae in the mainstream were slightly lower than those of the tributaries of the Yarlung Zangbo River Basin. The Shannon-Wiener diversity index varied from 4.84 to 9.41, and the Pielou evenness index varied from 2.41 to 4.80, indicating that the investigated water area was light pollution-clean water. The biodiversity characteristics and the P-IBI evaluation system of periphyton algae in the Yarlung Zangbo River Basin indicated that the water ecosystems in the upper, lower reaches of the main stream and four major tributaries were better than those in the middle reaches of the main stream of the Yarlung Zangbo River Basin. These results provide a basis for studying feeding habits and mechanisms of Tibet indigenous fishes to ensure the safety of water ecology and to realize the sustainable development of resources and environmental protection.