Background <p>Plant-associated microorganisms can enhance crop growth and resilience to environmental stressors. Maize (<i>Zea mays</i> L.) selectively recruits beneficial microbes under saline–alkali stress; however, the interplay between maize genotypic variation and microbial community dynamics remains poorly understood. Here, we compared the structure, diversity, and functional potential of root-associated microbial communities across eight maize inbred lines differing in saline–alkali tolerance.</p> Results <p>Compared with the saline–alkali-sensitive lines, the saline–alkali-tolerant lines exhibited significantly higher plant biomass and less leaf and root damage. Microbial communities in tolerant lines exhibited greater diversity and more complex co-occurrence networks, showing inferred functional enrichment in energy metabolism and antioxidant pathways. Genotype-specific recruitment of the beneficial bacteria (<i>Luteolibacter</i>, <i>Agromyces</i>, and <i>Luteimonas</i>) and selective enrichment of Ascomycota and putative endomycorrhizal fungi across the rhizosphere–root interface could collectively enhance host tolerance through improving nutrient mobilization, pathogen resistance, and stress mitigation. Moreover, we uncovered significant cross-compartmental co-occurrence patterns within and between bacterial and fungal communities, and revealed that saline–alkali-tolerant maize genotypes recruit functionally complementary microbiomes along the soil–root continuum. Aboveground traits appeared to shape community structure, whereas root endophytic bacteria were predicted to be linked to soil salinity, and fungi were associated with host plant stress tolerance.</p> Conclusions <p>These findings advance our understanding of genotype-dependent plant–microbe interactions under saline–alkali stress and provide actionable targets for the development of microbial inoculants for sustainable agriculture.</p>