Scratched alkyd varnish coating (AVC) with isophorone diisocyanate (IPDI) microcapsules as functional additives display self-healing properties. Here, we investigated the mechanism of the self-healing process using a water trigger in seawater. FT-IR spectra of the self-healing products in the scratched crevice confirmed that the scratched crevice was healed by self-healing product. Scanning micro-reference electrode (SMRE) and alternating current scanning electrochemical microscopy were used to monitor the self-healing process of IPDI-AVC. This study enhances the comprehension of the self-healing mechanism of self-healing AVC-coatings functionalized by the addition of microcapsules.