Isophorone diisocyanate-loaded microcapsules were synthesized with controllable size for self-healing of structural polymer materials. The obtained microcapsules showed good compatibility with polymer resins, e.g., one-component epoxy and multi-component polyurethane/water glass structural materials. During the processing of composite self-healing materials, the highly cross-linked composite capsule wall ensured the integrity of microcapsules and prevented the leakage and degradation of reactive liquid isocyanates effectively. A relatively larger amount of self-healing agent could be released to the local cracks with the increasing size and content of microcapsules in polymer matrix which improved the self-healing efficiency of the composites. Based on the microcapsules with a diameter of similar to 96m, the healing efficiency of epoxy composites containing 15 wt% of capsules and polyurethane/water glass composites containing 20 wt% of capsules could reach to 105 and 101% recovery of fracture toughness, respectively. The crack-healing effect was further verified by scanning electron microscopy. Meanwhile, a possible self-healing mechanism of microcapsules to the cracks of composite polymer materials was proposed.