Smart self-healing coatings have been attracting tremendous interest due to their capability for preventing crack propagation in the protective coatings by releasing active agents like isocyanate molecules from micro/nanocapsules. The quality of healed area and subsequent use of the healed coated module are directly related to the chemical composition of healing agent. Faster curing rate and more appropriate physical properties were anticipated for moisture curing of bulky isocyanate molecules than the low molecular weight monomeric analogous. For practical utilization of these advantages, encapsulation of such bulky isocyanate molecules was considered in this work. To this end, optimized preparation and characterization of novel single-layer polyurethane-type microcapsules, richly and efficiently loaded with bulky isocyanate molecules is described. This healing agent was prepared through the reaction of excess amount of isophorone diisocyanate (IPDI) with 2-ethyl-2-hydroxymethyl-1,3-propanediol (TMP). The healing agent was then encapsulated with a polyurethane shell via an oil-in-water (O/W) emulsion polymerization technique. The mixing rate and surfactant concentration were altered to optimize the size and shell thickness of the microcapsules. The prepared microcapsules were very stable after 10 months, and they just lost less than 7 wt% of their loaded isocyanate molecules. The microcapsules were loaded into an epoxy-based coating and the crack healing efficiency of incorporated healing agent was clearly recorded. Microcapsules containing monomeric IPDI were also prepared and crack healing efficiency of these two healing agents regarding crack healing was compared.