The phylogenetic structure of communities is a fundamental component in our ability to understand community assembly processes and species coexistence. However, although there have been many studies of the spatial and temporal variation in community structure, few have applied these observations to the dynamics of phylogenetic structure. Here, we performed such an analysis to study temporal and spatial variations in the phylogenetic structure of Fagus hayatae communities, Class Ⅱ protected plant, in China. In 2006, all free-standing woody stems with a diameter at breast height (DBH) ≥ 1cm were tagged, mapped, identified, and measured for DBH, and height in a 1 hm² forest dynamic plot in Qingliangfeng National Nature Reserve, China. This was followed by re-censuses in 2011 and 2016, in which we recorded the survival status and DBH for previously recorded stems and documented new stems with DBH ≥ 1cm. On the basis of these three censuses spread across a decade (2006, 2011, 2016), we measured the dynamics of the phylogenetic structure at three spatial scales (10m, 20m, and 50m). We used global seed plant phylogenetic data to construct a phylogenetic tree of F. hayatae communities, and selected the mean phylogenetic distance (MPD), mean nearest taxon distance (MNTD), net relatedness index (NRI), and nearest taxon index (NTI) to describe the phylogenetic structure of F. hayatae communities. Additionally, we randomly resampled 999 plots at 10m, 20m, 50m scales using a moving split-window technique to create plots at different spatial scales. Analysis across spatial and temporal scales produced the following results. (1) On decadal time scales, the species richness and abundance of F. hayatae communities both decreased. MPD decreased, whereas MNTD increased. NRI and NTI both significantly positively increased at large scales, but did not change at small scales. (2) As the spatial extent of analyses increased, so did the strength of the trends observed. Thus, the phylogenetic structure of F. hayatae communities showed a clustering pattern and was spatial scale dependent. The largest variation in the phylogenetic structure across time was found at the 50m scale. We concluded that from 2006 to 2016, the phylogenetic structure of F. hayatae communities was clustering, whereas the phylogenetic relationships between nearest species became more distant. Moreover, the effects of environmental filtering dominated the phylogenetic structure dynamics of F. hayatae communities at large scales. This is in contrast to the effects of stochastic processes and interspecific competition, which dominated at small scales. Against a background of global climate change and forest degradation, further studies on scale dependence are needed to gain a better understanding of the mechanisms of community assembly, and to protect these endangered species.