In this paper, the superhydrophobic poly(vinylidene fluoride)/fluorinated ethylene propylene/SiO2/CNTs-EDTA (PFSC-EDTA) composite coating was successfully fabricated and applied for anti-scaling performance. The deposition of CaCO3 on the surface of the superhydrophobic PFSC-EDTA composite coating reached 0.0444 mg/cm2 for 192-h immersion into the supersaturated CaCO3 solution, which was only 11.4% that of the superhydrophobic PFSC composite coating. At the interface between the CaCO3 solution and the PFSC-EDTA coating, the Ca2+ could be firstly chelated by EDTA that was benefit for improving the anti-scaling performance of the superhydrophobic PFSC-EDTA composite coating. In another hand, the addition of EDTA to the CNTs played an important role in fabricating the SiO2-centric and CNTs-EDTA-surrounded multilevel micro–nanostructure in the superhydrophobic PFSC-EDTA composite coating, in favor of maintaining the air film under the water and the stability of the superhydrophobic surface. The research supplies a new way of improving anti-scaling performance of superhydrophobic coating by incorporating the organic chelating agent at the interface and changing the traditional way of scale prevention.