The objective of this study is to investigate the evolution of asphalt morphology and adhesion properties during stress relaxation using atomic force microscopy (AFM) and molecular dynamics (MD) simulations. Changes in surface roughness, Derjaguin-Muller-Toporov (DMT) modulus, adhesion force, and force-distance curves were analyzed. Morphological and adhesion property evolution was assessed using correlation length and Lyapunov exponent. MD simulations provided insights into the internal stress-time relationship and free volume fraction of asphalt during relaxation. Results indicate that under constant tensile strain, the “bee structure” on the asphalt surface elongates, dark pits transform into light protrusions, microcracks heal, and surface roughness stabilizes after 10 h. Under compressive strain, similar changes occur but are more pronounced during tensile relaxation. The combined use of AFM and MD simulations offers a comprehensive understanding of the microscopic evolution mechanisms of asphalt under stress relaxation, providing valuable insights for optimizing asphalt pavement design and maintenance.