The growth and adaptability of desert plants depend on their rhizosphere microbes, which consist of a few abundant taxa and numerically dominant rare taxa. However, the differences in diversity, community structure, and functions of abundant and rare taxa in the rhizosphere microbiome of the same plant in different environments remain unclear. This study focuses on the rhizosphere microbial communities of Artemisia desertorum, a quintessential desert sand-stabilizing plant, investigating the diversity patterns and assembly processes of rare and abundant taxa across four Chinese deserts: Mu Us, Kubuqi, Tengger, and Ulan Buh. The results show that climatic factors, especially aridity and mean annual precipitation (MAP), significantly influence bacterial community composition and microbial network complexity. The interactions between rare and non-rare taxa are non-random, forming a modular network in which rare taxa serve as central nodes, and their loss could destabilize the network. Rare taxa are primarily shaped by heterogeneous selection, whereas abundant taxa are mainly influenced by dispersal limitation. Functionally, abundant taxa exhibit higher metabolic potential, whereas rare taxa are more involved in processes such as cell motility, indicating distinct ecological roles. These results provide new insights into the ecological functions of rare and abundant taxa in desert rhizosphere communities and highlight the importance of microbial management for desert plant health.