The key to engineering safety and disaster prevention in loess regions lies in precise characterization of loess stratigraphic permeability. This study selected a representative loess profile (containing multiple paleosol layers) to systematically acquire microstructural images at varying depths and directions via scanning electron microscopy. Integrated with saturated permeability test data, quantitative relationships between microstructural parameters and hydraulic properties were established. The results demonstrated significantly higher saturated hydraulic conductivity in loess layers compared to underlying paleosols, with enhanced vertical permeability capacity revealing marked anisotropy. Permeability disparities were governed by pore fabric evolution: loess layers predominantly contained continuous percolation networks composed of elongated and irregular meso-/ micropores, whereas paleosol layers developed discrete rounded micropores. With increasing depth, both porosity and equivalent pore diameter exhibited decreasing trends, while pore morphological complexity intensified. Principal component analysis identified permeability-sensitive parameters, enabling development of a microstructure-based permeability assessment model that provided scientific basis for precise stratigraphic permeability evaluation. The study further revealed unique engineering geological effects at loess-paleosol interfacial transition zones: their microporosity-enriched characteristics formed hydraulic barriers inducing unsaturated zone moisture accumulation, offering novel microstructural criteria for loess geohazard early warning. The established microstructure-permeability coupling model provided theoretical support for engineering design and disaster mitigation in loess regions.