The invention relates to a molybdate doped polypyrrole / epoxy resin self-healing coating, a preparation method thereof and an application thereof, and belongs to the field of metal anti-corrosion coatings. The coating is composed of two parts, namely a polypyrrole / epoxy resin system mother liquor, and a polyamide curing agent. The polypyrrole / epoxy resin system mother liquor comprises molybdate doped polypyrrole, epoxy resin, an anti-settling agent, an anti-foaming agent, a levelling agent and an organic solvent. The molybdate doped polypyrrole is added in the organic solvent and then the mixture is uniformly dispersed in an ultrasonic dispersion instrument. After that, the anti-settling agent, the antifoaming agent and the levelling agent are added respectively, and are stirred on a magnetic stirring apparatus. Then the epoxy resin is added to form the uniformly dispersed polypyrrole / epoxy resin system mother liquor. The polyamide curing agent is added in the prepared mother liquor, and is stirred to be uniformly dispersed. In this way, a molybdate doped polypyrrole / epoxy resin self-healing coating can be obtained. The coating is sprayed or brushed onto the 2024 type aluminum alloy after being subjected to oil-removing treatment. After the drying and curing process of the coating at the room temperature, a molybdate doped polypyrrole / epoxy resin self-healing coating can be formed.