In most grassland ecosystems, the effects of mean temperature increase on plant communities have been investigated; however, the effects of climate fluctuations on local plant community metrics are much less well understood. We conducted a nine-year survey in alpine meadow and alpine steppe to investigate the effects of inter-annual temperature and precipitation variation on plant community composition, species richness, and species diversity on the central Qinghai-Tibetan Plateau, China. We unexpectedly found that annual variability of growing season temperature, and not precipitation, is a driver of plant composition and species diversity in both habitats. Generally, increasing temperature had a negative effect on species diversity in meadow (r2 = 0.94) and steppe (r2 = 0.95). In the meadow habitat, the proportion of grass decreased with increasing temperature and ultimately had positive impacts on the proportion of sedges. In steppe habitat, legumes increased and forbs decreased with the increase of growing season temperature; both legumes and forbs negatively affected proportion of grass and resulted in grass remaining stable under temperature change. Our results provide evidence that responses of functional group composition and species richness to temporal change of temperature are very different from those responses to mean temperature increase on the central Qinghai-Tibetan Plateau. In our results, temperature is a main regulator for annual variation of functional group composition and species richness, while soil water content is a dominant regulator for community responses in other experimental warming studies.