Self-healing material is usually used as a mechanical component, which not only needs to consider the topological optimization of the macro-configuration of the structure, but also needs to consider the influence of the size and distribution of self-healing agent carrier microcapsules on the mechanical properties and healing effect of self-healing material. Therefore, the collaborative optimization of structural macroscopic configuration and internal microcapsules is of great significance. The research is based on Movable Morphable Component, for isotropic material object, using structural compliance as the objective function, the material area as constraint conditions, the establishment of a built-in microcapsules component two-dimensional mathematical model, based on the method of moving asymptote (MMA), collaborative optimization design method of self-healing materials is given, and compared with the classic self-healing materials, the superiority of collaborative optimization is verified. The results show that: (1) The configuration of two self-healing materials is similar; (2) The structural compliance of the two kinds of self-healing materials increased with the increase of microcapsule volume fraction, and the mechanical properties deteriorated to different degrees; (3) Compared with the classical self-healing materials, the collaborative optimized self-healing materials showed more excellent mechanical properties with the increase of volume fraction. When the volume fraction was close to 14%, the compliance of the collaborative optimized self-healing materials was only 66.1% of that of the classical self-healing materials.