The Three River Headwater region of Qinghai province, also known as the Qinghai-Tibetan Plateau is one of the regions in China likely to be most significantly affected by climate change. Hence, understanding the relationship between plant community distribution patterns and environment factors could afford scientific evidence for predicting the effect of climate change on plant diversity. In this research, six sites at a range of elevations and including 78 alpine meadow plots in the Three River Headwater region were surveyed to study the relationship between plant community structure and the environment. We aimed to explore the potential plant responses to climate change using a strategy of space-for-time substitution. At the six sites a total of 74 plant species belonging to 21 families and 51 genera were identified. Cyperaceous plants such as Kobresia schoenoides, Kobresia pygmaea and Kobresia humilis were the dominant species in the middle-high-elevation area, while plants of the Poaceae such as Stipa capillata, Poa annua and Elymus nutans covered the most of low elevation area. Species diversity index and richness index of the alpine meadow sites showed a unimodal pattern, and species evenness showed no significant differences along with the altitudinal gradient across the six sites. Detrended correspondence analysis indicated that species composition and diversity of plant communities changed continuously with decreasing elevation from alpine meadow to alpine steppe meadow. In addition, canonical correspondence analysis showed that soil pH was the main factor affect species diversity patterns in alpine meadow. Meanwhile, soil moisture, temperature, organic carbon content, available nitrogen content and total potassium content were key factors affect the distribution patterns of plant communities. On the basis of these observations, we predict that climate change is very likely to change plant community structure in the Three River Headwater Region.