A microcapsule-type self-healing protective coating with secondary crack preventing capability has been developed using a silanol-terminated polydimethylsiloxane (STP)/dibutyltin dilaurate (DD) healing agent. STP undergoes condensation reaction in the presence of DD to give a viscoelastic substance. STP- and DD-containing microcapsules were prepared by in-situ polymerization and interfacial polymerization methods, respectively. The microcapsules were characterized by Fourier-transform infrared (FT-IR) spectroscopy, optical microscopy, and scanning electron microscopy (SEM). The microcapsules were integrated into commercial enamel paint or epoxy coating formulations, which were applied on silicon wafers, steel panels, and mortar specimens to make dual-capsule self-healing protective coatings. When the STP/DD-based coating was scratched, self-healing of the damaged region occurred, which was demonstrated by SEM, electrochemical test, and water permeability test. It was also confirmed that secondary crack did not occur in the healed region upon application of vigorous vibration to the self-healing coating.