Aim Understanding patterns and drivers of phylogenetic beta diversity in a region is important to understanding the origin and maintenance of the regional species diversity and variation in species diversity between local sites. Here we used a phylogenetic beta diversity metric quantifying deep evolutionary histories to explore geographical and ecological patterns of phylogenetic beta diversity in angiosperm assemblages across China. Location China. Taxon Flowering plants (angiosperms). Methods China was divided into 100 x 100 km grid cells. Species composition in each grid cell was documented. We used a basal-weighted metric (D-pw) to quantify phylogenetic beta diversity among angiosperm assemblages with two sampling approaches (neighbourhood approach and pairwise approach). D-pw was related to latitude and climatic conditions of angiosperm assemblages and to geographical and climatic distances between angiosperm assemblages across China. Results We found that the southeastern portion of China has much higher D-pw than the northwestern portion of China. The line of high versus low values of D-pw across China is generally consistent with the line of 500-mm precipitation per year. Our study shows that precipitation is associated with D-pw more strongly than temperature, and D-pw decreases with latitude, particularly in the eastern part of China. Main conclusions The emergence of the observed pattern of basal-weighted phylogenetic beta diversity is at least partly because the southeastern portion of China retains a large number of Tertiary relicts, making it a biogeographical museum, whereas many Tertiary relicts went extinct from the northwestern portion of China, particularly the Tibetan Plateau, due to the uplift of the plateau and the Himalayas, which makes the region a biogeographical grave for Tertiary relicts.