Waterborne two-component epoxy coatings with good appearance and performance on the substrate with residual waterborne rust inhibitor was developed to solve theissue of deteriorating coating quality caused by residual waterborne rust inhibitor on thesurface of metal substrate. The effects of waterborne epoxy resin，wetting agent，co-solvent and functional filler on the performance and appearance of the coating were studied. The resultsshowed that the main resins of the coating system were YPWE-406 A and AEH-20，which were compounded according to the mass ratio of 1∶3，0. 2%HOS 2413 and 0. 4% Dynol-607 were added as the wetting agent，6% compound solution（a mixture of IPA，PNB and DPNB in a 1∶1∶1 mass ratio）and 5% flake structure filler were added，then the waterborne two-component epoxy coatings with best performance were obtained，which could solve the coating problem ofwaterborne two-component epoxy coatings on the substrate with residual waterborne rust inhibitor.