Waterborne protective coatings have attracted tremendous attention recently, but their practical applications are severely limited by week shielding performance and poor mechanical durability. Herein, a concrete-like three-dimensional network filler was designed by stacking fly ash, graphene oxide, and multi-walled carbon nanotubes onto each other with the help of a silane coupling agent to enhance the anti-corrosion performance and wear resistance of waterborne epoxy coating. Through chemical modification, the surface of the filler has a large number of both epoxy and amino groups, and the filler-filler, resin-filler, and resin-resin multi-dimensional cross-linking reactions occur inside the coating to improve the cross-linking performance of the water-based resin. With the help of the stable structure of the “imitation” concrete structure and greater interface strength of the silane-modified composite material, the water-based coating exhibits excellent anti-corrosion and wear resistance. The mass loss of the imitation concrete coating is only 0.0098 g per-cycle of Taber friction testing, and in the electrochemical impedance spectroscopy test, its |Z|0.01 Hz value became stabilized at approximately 1 × 107 Ω·cm2 after 14 d of being immersed in 3.5% NaCl solution, and its value was two orders of magnitude higher than that of pure epoxy. The results show the matching of the three different types of fillers in the imitation concrete, and interface chemical control of the filler surface can improve the compatibility between the functional filler and water-based epoxy resin. The use of industrial waste fly ash as one of the main fillers is conducive to promoting the recycling of resources, so that the coating has a certain cost performance and engineering application value. This study is expected to open new insights into specialized design of the internal filler of such coatings and the modification of the internal surface of a water-based coating improves the coating’s anti-corrosion and wear resistance.