Soil salinisation has become a global environmental problem, seriously threatening the stability and sustainable development of regional ecosystems. As a key tree species for the ecological restoration of saline‒alkali lands, investigating the root-associated microorganisms of Elaeagnus angustifolia L. provides an important approach to addressing this challenge. This study integrates non-targeted metabolomics and high-throughput sequencing technologies to systematically analyse the composition, diversity and characteristics of bacterial communities in different ecological niches of E. angustifolia roots in the Bayingolin Mongol Autonomous Prefecture, Xinjiang, China (rhizosphere, non-rhizosphere, root endophytic and peri-root soil), aiming to identify core functional bacterial communities and clarify the root-bacteria interactions. The results show that Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidota are the key groups for E. angustifolia to improve saline‒alkali soil; the diversity (abundance-based coverage estimator (ACE), Shannon, Simpson index) of bacteria in rhizosphere, non-rhizosphere and peri-root is significantly higher than that of root endosphere communities and the soil bacterial symbiotic network is more complex and stable, while the richness of rhizosphere and non-rhizosphere is similar. Root exudates were closely associated with bacterial genera including Bosea, Chryseolinea, Candidatus Solibacter, Steroidobacter and Ramlibacter. The study provides a theoretical basis for the exploration of beneficial microbial resources of E. angustifolia in Xinjiang and the biological restoration of regional saline‒alkali land.