Interface properties between asphalt and aggregate intimately affect the service performance and long-term durability of asphalt pavement. This study seeks to explore the interfacial adhesion features of high-viscosity asphalt (HVA)-aggregate under water conditioning to provide the understanding for the moisture damage of HVA-aggregate interface and asphalt pavement. To this end, the HVA was initially suffered from different durations of water conditioning, and atomic force microscopy (AFM) test was employed to gather the microscopic phase structure and adhesion force of water-conditioned HVA and aggregate, to analyze the adhesion variations of HVA-aggregate interface. Further, molecular dynamics method was used to simulate the changing process and influencing mechanism of adhesion effect at the HVA-aggregate interface under water immersion. The findings indicated that with the increasing water immersion, Catana phase of HVAs vanished, and concave and convex structures appeared on the surface, along with pit groove dispersion phase structures. Longer immersion time resulted in augmented surface roughness of HVA and a more dispersed height distribution in the area domain, most notably during the initial stages of water immersion. Aging increased sensitivity to immersion duration in terms of surface roughness, mechanical properties and adhesion ability of HVAs. Water immersion had a diminishing effect on the mechanical properties of HVA at different aging degrees, although it increased the micro-mechanical modulus of HVAs and impaired the interface adhesion with aggregates. Under water immersion, the phase structure and mechanical properties of HVAs and the interface adhesion indexes all distinguished a prominent negative Pearson correlation (correlation coefficient |R| > 0.7000), and these factors were critical for HVA-aggregate interface adhesion, as alterations in surface phase structure and micro-mechanical traits of HVAs triggered variations in the HVA-aggregate interface adhesion. In addition, water content in the interface layer, simulation temperature and mineral anisotropy significantly affected the interfacial adhesion of HVA and aggregate in water environment. The introduction of water and the rise of temperature considerably weakened the interfacial adhesion effect of asphalt-aggregate system, and the interface adhesion failure occurred once the water layer thickness surpassed 5 Å. Comparatively, the HVA-calcite system demonstrated better interfacial adhesion competence than the HVA-α-quartz system, and the HVA-calcite {1 0 4} system showed the optimal interfacial adhesion.