With the development of agriculture and the widespread application of agrichemicals in Tibet, herbicide residues have become a threat to the ecological safety of Tibetan water bodies. Algae, as the producers in the food chain in water bodies, play an important role in aquatic ecosystems. Therefore, the impact of herbicides on Tibetan algae is of great significance for evaluating ecological health and the protection of Tibetan water ecosystems. In this study, we investigated the inhibitory effect of glyphosate, a herbicide, on the photosynthetic system of Chlorella vulgaris, Tibetan algae, by determining chlorophyll fluorescence and the activity of an antioxidant system. The results revealed that glyphosate at low concentration did not affect the photosynthetic activity of C. vulgaris; however, glyphosate at a high concentration significantly inhibited photosynthetic activity and reduced pigment content. Moreover, high levels of glyphosate also decreased photochemical efficiency and electron transport rate and resulted in ROS accumulation, high SOD activity, and lipid peroxidation. These results suggested that glyphosate could decrease the primary production of aquatic ecosystems and influence their performance. Therefore, reducing the herbicide levels could protect the Tibetan aquatic environment and maintain the health of ecosystems.