Asphalt pavements at high-altitude airports endure prolonged extreme low temperatures and large diurnal swings, imposing stringent demands on crack sealants, whose multi-scale adhesion failure mechanism remains unclear. Three SBS and crumb-rubber-composite-modified sealants, designated A, B and C, were characterized through surface free energy tests, pull-off and shear tests, fluorescence microscopy, FTIR and molecular dynamics simulations. Cross-scale correlation analysis and CRITIC-TOPSIS were applied to link and rank the sealants across scales. Work of cohesion, work of adhesion, pull-off strength and shear strength all rose monotonically with modifier content, and sealant C exhibited a 38.5% higher work of cohesion and a 52.4% lower CV_φ than sealant A. Molecular dynamics simulations showed that electrostatic forces drove sealant–aggregate adhesion while van der Waals forces governed sealant–asphalt adhesion, with a simulation–experiment deviation of only 2.88–5.74%. A level-by-level transmission linked phase-morphology uniformity, intermolecular interaction, interfacial energy and macroscopic mechanical performance. Sealant C achieved a CRITIC-TOPSIS index of 1.000, far above 0.271 for B and 0.000 for A, and is recommended as the preferred material for crack sealing of high-altitude airport asphalt pavements.