The preparation and application of microcapsules containing healing agents have become a crucial way to enhance the self-healing capability of bitumen. This intelligent material has become a hot topic in the field of pavement material and has greatly stimulated the development and applications of pavement engineering. However, there has been no research focused on the relationship of the multistructures from the viewpoint of molecular-size, microsize, and macrosize, which significantly limits the predictions of the self-healing efficiency and structure design of this self-healing material. The purpose of this study was to make a mathematical analysis of the influencing factors of self-healing efficiency based on the self-healing mechanism of bitumen using microcapsules, fully considering the structural dimensions, preparation conditions, and self-healing conditions. In the mathematical analysis, the cross-linking degree of the shell material molecules of the microcapsules was considered for its damage strength from the perspective of molecular structure. The final tip stress of the microcrack was believed to be equal to the puncture strength of the microcapsules in terms of microsize. From a macroscale point of view, the amount of healing agent released from the microcapsule rupture was considered more significant than or equal to the volume of the microcracks. At the same time, the time–temperature superposition principle was applied to simplify the influence factors. The above derivation based on multiscale structures found that the additive amount of the microcapsules, temperature, and time were the three main influencing factors on the self-healing features of bitumen. Finally, the experimental data was investigated considering the three factors, which thoroughly verified the feasibility of the derivation. All results will help to establish a bridge between the initial structural design of self-healing bitumen and the prediction of the final self-healing effects.