In the typical dry valleys of the Three Parallel Rivers region, northwest Yunnan Province, we investigated vegetation using six sampling transects, each comprised of ten standard plots, along altitudinal gradients on the eastern and the western aspects of Nu River, Langcang River, and Jinsha River. With these data, we compared the elevation-related distribution of plant species richness and species turnover rates along the six transects, and explained the patterns using geography and vegetation variables. The dry-warm vegetation zone was dominated by shrubs and herbs and located below the altitude of 3,000 m a.s.l. At higher elevations, shrub and herbs were replaced with a forest zone. The spatial distribution of plant species richness increased with elevation and latitude, especially for herb and shrub species, and was also related to river, vegetation zones, and longitude. The species richness of shrubs also increased significantly across the region, from west to east. Species richness of herbs and shrubs in the Nu River were higher than those in the Lancang River and the Jinsha River, whereas the difference of species richness among three rivers was not significant for trees. Herb species richness in the forest zone was less than that in the shrub and herb zones. Species turnover rate of different zones presented inconsistent altitudinal gradient patterns, but all peak values appeared in the ecotones between shrub communities, in the lower altitudes of the transect, and forest communities, in the higher altitudes. The forest-shrub ecotone is located at an altitude range of 1,900-2,100 m in the Nu River valley, at an altitude range of 2,300-2,400 m in the Lancang River valley and at an altitude range of 2,700-2,900 m in the Jinsha River valley. The mean species turnover rates between shrub & herb section and forest section within each transect were less than the mean turnover rates of the same vegetation section between different transects within the same basin, and also less than the mean turnover rates for same vegetation section in all six transects. Spatial isolation could explain 34.2% of the variation in species turnover rate among the 12 vegetation sections of the six altitudinal transects, while vegetation differences explained less than 0.5% of the variation. These results show the primary role of environment difference in determining the species richness between vegetation types, whereas geographical isolation between the rivers as a dominant factor in the assembly (e.g. species composition) of plant communities.