The bee structure of an asphalt binder surface changes during the aging and rejuvenation process, and the effect of this microstructural change on the mechanical properties of the asphalt binder is not clear. Therefore, in this paper, a two-dimensional finite element model of an asphalt binder microstructure was constructed based on processed AFM images, and the contents of bee phases and bee casings were varied at the same time to analyze the stress and strain distribution law of the asphalt binder microstructure. The results of the study show that in the bee structure, the stress in the bee phase is obviously greater than that in the bee casing, and the stress in the interstitial phase is the lowest. With the simultaneous enhancement in the proportion of the bee phase and the bee casing, the stresses in the asphalt samples increased in all phase structures. Under the combined effect of the decrease in the content of the bee phase and the increase in the content of the bee casing, there is a certain degree of increase in the internal stresses and strains in the asphalt binder, the effect of the bee casing on the internal stresses in the asphalt binder is more pronounced, and the bee phase and the bee casing play better roles in resisting the external deformation due to the increase in the volume fraction. For a recycled asphalt binder, whether there is an increase in the dosage of the old asphalt binder or an enhancement in the interfacial diffusion and a fusion of new and old asphalt binders, the level of tensile strain within the recycled asphalt binder will increase to a certain extent, which, in turn, will put forward a higher requirement for its anti-cracking ability.