Although plant-associated microbes influence plant performance and ecological adaptability, knowledge of microbial variation between the root endosphere and rhizosphere of desert relict plants remains limited. Ammopiptanthus mongolicus, a relict species native to the hyper-arid deserts of northwestern China, was used to investigate microbial community structure across ecological niches and their soil ecological responses, aiming to elucidate adaptive plant-microbe symbioses and microbial distribution patterns. Root and rhizosphere soil samples were collected from Wuhai and Alxa in July 2021 to characterize microbial assemblages. Pronounced differences in community composition were observed between niches, with significantly higher species richness and alpha-diversity in the rhizosphere. PCoA indicated that niche type was the primary driver of microbial differentiation, outweighing site-level effects. Although more enriched taxa occurred in the rhizosphere, differentially abundant fungal taxa were far fewer than bacterial taxa. Co-occurrence network analysis showed that positive interactions dominated microbial associations, with the rhizosphere network exhibiting greater complexity, while endosphere fungal communities showed positive associations. Six low-abundance OTUs (< 0.1%) functioned as keystone taxa supporting network stability. AP, SOC, NH4 +-N strongly shaped bacterial and fungal communities. Pathotrophs and saprotrophs dominated fungal guilds, whereas intracellular parasites and chemoheterotrophs prevailed among bacteria, with symbiotic fungi enriched in the endosphere.