Periphytic algae constitute integral components of river ecosystems, serving as a starting point in the food chain of aquatic ecosystems. They play a crucial role in maintaining ecological diversity, energy flow, and material transfer within ecosystems. Benthic algae respond rapidly to anthropogenic disturbances and environmental changes, and are widely used in river biodiversity monitoring and water environment assessment. Comparing the species composition and distribution among periphytic algae communities in different rivers along with elucidating their relationships with riverine environments, contributes to a better understanding of mechanisms maintaining river biodiversity. Therefore, we sampled periphytic algae from 38 sites in the main tributaries of the upper Jinsha River (i.e., Sequ River, Zengqu River, Ouqu River and Zangqu River) during May and June of 2021, and recorded their environmental conditions. The influence of environmental factors on the community structure of periphytic algae was analyzed using the redundancy analysis method. Results revealed 91 taxa of periphytic algae, belonging to 3 phyla and 34 genera, with Bacillariophyta as the most species-rich group. Periphytic algae density in the major tributaries of the upper Jinsha River varied from 0.002×10⁵-2.43×10⁵ cells/cm² and the biomass varied from 0.3×10^-3-1.56 mg/cm². No significant differences were found in benthic algae density and biomass among the various tributaries. In the Sequ River, dominant species included Lyngbya semiplema, Calothrix sp. and Navicula minima. In the Zengqu River, dominant species included Lyngbya semiplema, Diatoma tenue and Synedra tabulata. The Ouqu River exhibited dominant species such as Lyngbya semiplema, Fragilaria intermedia and Cymbella hustedtii. In the Zangqu River, the dominant species were Lyngbya semiplema, Lyngbya hieronymusii and Cymbella perpusilla. Redundancy analysis indicated that conductivity, pH, channel width and dissolved oxygen were the main driving factors affecting the community structure of the dominant taxa in main tributaries of the upper Jinsha River. These findings suggested that environmental filtering played a role in the spatial patterns of periphytic algae communities in the upper Jinsha River. This study provides basic data and a theoretical basis for the sustainable management and conservation of aquatic ecosystems in the main tributaries of the upper Jinsha River.