Atomic force microscopy (AFM) was used to explore the effects of graphene modifier on the microstructure of asphalt. The morphologies of the before- and after-aged base asphalt and modified asphalt were performed and compared with analysis. The formation mechanism of asphaltic “bee structures” and the influence mechanism of graphene on asphalt were discussed from the classical theory of material science (phase transformation theory and diffusion theory). The results show that graphene facilitates the nucleation of “bee structures”, resulting in an increasing number and decreasing volume of “bee structures” in modified asphalt. Additionally, the anti-aging performance of the modified asphalt improved significantly because of graphene incorporation.