As alpine plants, cushion species are particularly susceptible to environment changes. Thus, understanding population structure and community diversity variation of cushion plants along elevational gradients is crucial for estimating their response to predicted climate changes. In this study, Thylacospermum caespitosum populations from three elevations (low, medium, and high) in three climate zones of China (the Kunlun, Qilian, and Tianshan Mountains) were selected to evaluate the effect of elevation on the structure of T. caespitosum populations and species diversity of cushion communities. Results showed that elevation substantially influenced T. caespitosum populations (size structure, density, and death rate), as well as richness (α-diversity) and microhabitat species pool (species pool) of cushion communities. In the low elevations, T. caespitosum populations were in decline due to a lower ratio of small plants and higher mortality compared with populations at medium and high elevations. The α-diversity and species pool in cushion communities were significantly increased with decreased elevation, but the importance value of T. caespitosum decreased accordingly. Moreover, there was a significant positive  orrelation between elevation and relative importance value (the importance of one species in the community) of T. caespitosum (r = 0.883; P < 0.01). Elevation was significantly negatively correlated with the mortality rate of T. caespitosum (r = - 0.855; P < 0.01), α-diversity (r - 0.933; P < 0.001), and species pool (r = - 0.885; P < 0.01). The declining characters of T. caespitosum population structure were obvious in low elevation populations. This decline may directly or indirectly relate to environmental change. Effects of elevation can provide an early indication of range contractions and population  declines of cushion species with future climate warming. We call for more mechanistic studies of climate change impacts on cushion populations, particularly in alpine systems near the snow line.