The Yalong River is the biggest tributary of the Jinsha River. Periphytic algae are an important component of the aquatic ecosystem, playing an important role in the energy flow and matter cycling of river food chains. To understand the community structure of periphytic algae and its relation to the environmental conditions, surveys were conducted in the lower Yalong River and its tributaries between June and August 2018 (102°6′6″E, 28°46′21″N–101°49′22″E, 26°38′38″N). A total of 95 species of periphytic algae belonging to 49 genera of five phyla were identified, among which Bacillariophyta (57 species) were the dominant taxa, followed by Chlorophyta (20 species) and Cyanophyta (14 species). The species richness was highest in the Yalong River, followed by the Anning River, and lowest in the Anning River tributaries. The dominant species in the lower Yalong River were Achnanthes sp., Gomphonema sp., Leptolyngbya gelatinosa, Synedra sp., Navicula sp., Oocystis naegelii, and Cymbella sp.; the dominant species in the Anning River were Achnanthes sp. and Aphanocapsa elachista; and the dominant species in the tributaries of the Anning River were Achnanthes sp., L. gelatinosa, Gomphonema sp., Navicula sp., and Cocconeis placentula. The algal density in the Yalong River was significantly lower than that in the Anning River and its tributaries. The algal density in the Anning River was higher than that in the tributaries. Upstream to downstream, the species richness in the Anning River increased under a longitudinal gradient, the proportion of Bacillariophyta in the Anning River decreased gradually, while the proportion of Chlorophyta and Cyanophyta increased gradually. Redundancy analysis indicated that the periphytic algae structure in the lower Yalong River was relative to the ecological factors, such as water temperature, turbidity, and substrate type. Current velocity and altitude were the main environmental factors affecting the distribution of periphytic algae in the Anning River under a longitudinal gradient. This study provides a scientific basis for the research on and conservation of biodiversity in high-altitude areas.