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. Electrochemical impedance spectroscopy was used to monitor the self-healing efficiency. A detailed examination of the penetration of seawater into the crevice, the self-healing process along the crevice, the self-healing process of seawater penetrating into the coating and failure process of the coating was carried out. The self-healing time of IPDI-AVC was influenced by different metal substrates and self-healing could be inhibited by active metals such as Q235 steel. Due to the formation of a thin metal-oxide layer on the metal surface, other metals, such as 5083 aluminum alloy, titanium and copper, had much less influence on the self-healing time of IPDI-AVC. This study enhances the comprehension of the mechanism of self-healing AVC functionalized by the addition of microcapsules.