An emerging technology to mitigate the cracking of asphalt pavements is the use of self-healing capsules embedded in asphalt mixtures. In this study, self-healing capsules were fabricated by encapsulating asphalt rejuvenators with calcium alginate shells. While past studies have used a “brute force” design process for such capsules, the design and formulation of these can be optimized through careful consideration of chemical interactions and crack healing mechanisms. In this study, experiments and molecular dynamics (MD) simulation were used to engineer capsule–rejuvenator formulations to mitigate premature failure of capsules and improve self-healing efficiency. To explore the thermodynamic process, the inter-diffusion coefficient and blending degree between materials in the capsule system were evaluated at different temperatures and capsule designs to determine the ratio of capsules which survive mixing and compaction through molecular scale studies. MD provided an understanding of healing behavior by simulating and quantifying the fracture–healing–fracture process of the binder–capsule system. The experiments verified the MD model by quantifying oil release percentage from micro-extraction and recovery and fine aggregate matrix (FAM) healing efficiency. The research revealed that the interaction between asphalt binder, rejuvenator, and capsules highly depended on their chemical compositions and that the dose of capsule content influences the penetration degree, and structural failure process. Polymeric capsules experienced significant premature failure and content release at high temperatures (160 °C) compared to intermediate temperatures (25 °C) due to enhanced thermal movement. To optimize capsule performance, rejuvenators C and E, which had higher viscosities, required 30%–40% calcium alginate, while rejuvenator A with lower viscosity needed 40%–60% calcium alginate. Rejuvenators with more asphaltenes were more sensitive to the capsule shell protection effect, and strengthened healing efficiency, while rejuvenators with more aromatics resulted in better wetting and diffusion processes during healing. The healing index, derived from FAM experimental healing test and validated by simulations, indicated that approximately 40% shell material effectively prevented capsule breakage and resulted in a 50% reduction in healing capacity. This research therefore established a framework for engineering a combination of capsules for use at pavement scale based on an understanding of chemical interactions, mechanical properties, and experimental verification.