Phylogenetic information is a critical component of community ecology and conservation biology. In order to explore the phylogenetic community structure of desert shrub and its relationship with environmental factors in the Qaidam Basin, we selected the shrub communities as the research objects and calculated the phylogenetic community structure with picante package in R based on the species presence/absence in the community, and analyzed its relationship with mean annual temperature, mean annual precipitation and soil water content to reveal the relationship of species coexisting shrub communities and mechanism of biodiversity maintenance. The results showed that: (1) there was a significant correlation (P=2.77×10^-6) between the phylogenetic structure of the shrub communities and the soil water content in the Qaidam Basin, which showed that the aggregation degree of the phylogenetic community structure decreased gradually with the increase of the soil water content (SWC), suggesting the effect of habitat filtration on communities structuring weakened and biological interactions strengthened gradually. (2) There were no significant correlation between the phylogenetic community structure and the mean annual temperature, mean annual precipitation. (3) There were significant differences in the phylogenetic community structure between shrubs in typical desert habitat and in river valley (river floodplain) habitat, respectively, and showing phylogenetic clustering and overdispersion, while the phylogenetic diversity of the shrub communities in river valley (river floodplain) habitat was also significantly higher than that of them in typical desert habitat. (4) Applying the community phylogenetic information to the practice of biodiversity conservation, we found that the shrub communities in river valley (river floodplain) habitat might have a higher conservation value than that in typical desert habitat. The study indicated that the integration of community phylogenetic research and conservation biology theory will make the biodiversity conservation strategy more scientific and efficient.