Enclosure (prohibition of grazing) is an important process to restore alpine grassland on the Qinghai-Tibetan Plateau. However, few studies have quantified the extent to which the long-term enclosure may contribute to the changes in plant phylogenetic diversity and community assembly in alpine grassland under environmental change. In this study, based on an 11-year fencing experiment along an altitudinal gradient ranging from 4400 m to 5200 m in central Tibet, we conducted an observation of species composition and coverage within and outside the fences in the fifth, eighth and eleventh year, and monitored the related climate and soil factors at 7 sites. Our aim is to quantify the relative effects of environmental change and grassland management on the alpine plant community assemblage. The results were: (1) the overall phylogenetic structure (NRI) of the alpine plant communities, whether inside or outside the enclosure, was divergent at altitudes where the environment was relatively unextreme (4800–5100 m), but aggregative at altitudes with low precipitation (4400–4650 m) or with low temperature (5200 m). (2) The phylogenetic structure of the nearest taxon of species (NTI) was more aggregative along the whole gradient. (3) Precipitation was the dominant factor driving the changes in species richness, phylogenetic diversity and community α-phylogenetic structure indices (NRI and NTI), followed by enclosure duration and soil C:N ratio. (4) The phylogenetic structure of the communities was similar at higher altitudes under grazing or enclosure treatments, and was opposite at lower sites. Stochastic processes have driven the changes in the communities between inside and outside the fences at all altitudes. In addition, homogeneous dispersal occurred in communities at higher sites. In summary, the 11-year enclosure had little effect on community structure of alpine meadows where the grazing pressure is relative lower, whereas it could help restore the community of steppe meadow at lower altitudes where the grazing pressure is extensively higher. This study may provide a vital theoretical support for the formulation of differential management for alpine grassland on the Tibetan Plateau.