Introduction Microorganisms regulate nutrient cycling and ecosystem stability in saline-alkali ecosystems. However, their adaptation mechanisms and metabolic functions to saline-alkali stress in agro-pastoral ecotones remain unclear. Methods We characterized bacterial and fungal communities in four typical saline-alkali habitats in the agro-pastoral ecotone of the Loess Plateau [saline-alkali flat (SAF), natural grassland, maize cropland, and shrubland] via Illumina MiSeq sequencing. We analyzed community compositions, alpha-diversity, co-occurrence network characteristics, and functional group differences, using Mantel tests, redundancy analysis (RDA), and partial least squares path to examine environmental drivers of microbial structure and function. Results Saline-alkali stress significantly altered soil physicochemical properties (P < 0.05), with SAF exhibiting higher pH, EC, Na+, and low available nutrients. Bacteria alpha-diversity differed significantly among habitats (P < 0.05), suggestive of sensitivity to saline-alkali stress. Under such stress, bacterial co-occurrence networks simplified with intensified interspecific competition, whereas fungal networks maintained high modularity (0.77-0.81) and were dominated by positive correlations (>93%), reflecting a synergistic coexistence. Functionally, saline-alkali stress inhibited bacterial chemoheterotrophy, aerobic ammonia oxidation, and nitrification. Saline-alkali stress also promoted fermentation, phototrophy, and nitrate reduction and jointly drove microbial functional expression, with pH, available phosphorus, and soil organic carbon (SOC) identified as key drivers (P < 0.05). Conclusion We identified adaptive strategies and functional differentiation of bacterial and fungal communities under saline-alkali stress. These findings provide important insights for the sustainable management and ecological restoration of saline-alkali lands in agro-pastoral ecotones.