As a novel pavement wear layer material, the micromechanical mechanisms of High-toughness Ultra-thin Friction Course (HUFC) have not been fully elucidated. This paper presents a new method for the three-dimensional micromechanical simulation of high-toughness asphalt mixtures based on a viscoelastic parameter calibration model. X-ray Computerized Tomography (CT) was employed to scan samples of high-toughness asphalt mixtures to obtain detailed information on the internal structure (aggregate, fine aggregate matrix FAM and voids), and a three-dimensional micromechanical model was constructed based on the real-scale distribution of these components. Aggregates in the high-toughness asphalt mixture were modeled as elastic bodies, while FAM was treated as a viscoelastic material characterized by the Burgers model. Using the Boltzmann linear superposition principle and Laplace transform theory, the viscoelastic properties of FAM were converted into Prony parameters recognizable by finite element software, and the viscoelastic parameters were calibrated. Micromechanical simulations were conducted for three different gradings of high-toughness asphalt mixtures, and the results show that the predicted deformation closely matched the measured deformation. This method accurately reflects the deformation characteristics of different gradings of high-toughness asphalt mixtures, overcoming the limitations of traditional numerical simulations based on homogeneous material models. It represents an advancement and refinement of micromechanical simulation methods for high-toughness asphalt mixtures.