Salt-alkali stress is a major constraint on maize (Zea mays L.) production in arid and semi-arid regions, where excess Na⁺ and high pH damage root systems, yet the vulnerability of distinct root modules remains poorly understood. This study resolved the root-order-specific patterns of Na⁺ accumulation, membrane injury, and lifespan reduction, together with their anatomical underpinnings. A two-year (2022–2023) field experiment was conducted using the maize hybrid Xianyu 335 on typical soda saline-alkali farmland in Alar, Xinjiang, China, with a freshwater-leached control (CK) and a sustained saline-alkali stress treatment (S). Using a branching-order separation technique, roots were classified into five root orders (I–V). We measured ion concentrations, anatomical and cell-wall traits (light microscopy and Fourier-transform infrared spectroscopy), membrane integrity via electrolyte leakage, and in situ root lifespan using minirhizotrons for each root order. Statistical analyses included two-way ANOVA, stepwise regression, principal component analysis (PCA), and Pearson correlation analysis to quantify treatment effects. Salt-alkali stress induced significant root-order heterogeneity in Na⁺ accumulation: first-order absorptive roots reached a Na⁺ concentration of 15.8 mg/g, 3.0 times that of third-order transport roots, while their K⁺/Na⁺ ratio dropped sharply from 9.3 to 0.3. Root order, saline-alkali stress, and their interaction explained 38.2%, 52.3%, and 9.5% of the total variance in Na⁺ concentration, respectively (P < 0.001). This differential Na⁺ accumulation was driven by anatomical divergences across root orders: first-order roots possessed a far thinner cortex (58 μm vs. 118 μm in third-order roots) and substantially lower lignification (only 35% of fifth-order roots). Cortical thickness and lignin content jointly explained 78% of the inter-order variation in Na⁺ concentration, which was strongly correlated with cortical thickness, lignin deposition, electrolyte leakage, and root lifespan. The adverse impacts of salt-alkali stress also differed markedly by root order: electrolyte leakage in first-order roots increased by 222%, and median root lifespan shortened from 19 d to 10 d. By contrast, fourth- and fifth-order roots only exhibited a 25% rise in electrolyte leakage and a 12.0% reduction in lifespan. PCA further verified that absorptive roots underwent a more dramatic shift along the stress-response gradient, and final grain yield was reduced by 45.8% under saline-alkali stress. These findings demonstrate that first- and second-order absorptive roots, due to weak apoplastic ion exclusion barriers, serve as the primary sites of Na⁺ accumulation. Accelerated functional deterioration of these absorptive roots constitutes a core pathway of salt-alkali damage to maize roots. This research provides a theoretical framework to transform saline-alkali soil amelioration strategies from simply boosting total root biomass to protecting the functional capacity of absorptive roots, and offers support for precise field management targeting specific functional root modules.