The formation of inorganic foulants can significantly impair the efficiency of desalination processes. For thermal desalination technologies such as multistage flash (MSF), scale formation often leads to increased thermal resistance of evaporator walls and clogging inside heating exchanger tubes. Consequently, the desalination plants have to be shut down regularly for maintenance, even though additives have been applied to control the precipitation rate of Ca- and Mg-containing minerals. Strategies to effectively reduce scaling on desalination equipment surfaces are therefore highly desired for energy-efficient uninterrupted desalination operations. Here, we developed anti-scaling surfaces using initiated chemical vapor deposited (iCVD) covalently crosslinked organic networks. These coatings are ultrathin so as to maintain the overall heat transfer coefficient. We analyzed the adhesion between iCVD polymers and CaCO3 single crystal surfaces using molecular force probe (MFP). We also investigated the heterogeneous nucleation of CaCO3 on untreated and iCVD-coated Cu/Ni alloy foils using ammonium carbonate diffusion method at room temperature as well as boiling precipitation tests in simulated MSF conditions. The total amounts of CaCO3 formed on substrate surfaces were quantified via inductively coupled plasma-optical emission spectroscopy (ICP-OES). The growth of CaCO3 on Cu/Ni foils coated with iCVD polymer thin films is as low as 0.58 μg/cm2 in boiling conditions after 2 h, which is up to 25 times lower than that on untreated Cu/Ni foils. Corrosion of Cu/Ni during exposure to aqueous solution at elevated temperatures was found to increase the heterogeneous nucleation of CaCO3. Our iCVD polymer coatings exhibit excellent protection for Cu/Ni surfaces from corrosion, low adhesion to CaCO3 single crystal surface, reduced CaCO3 nucleation rate and good stability in long-term boiling tests. Thus these iCVD thin films are very promising for scaling control in MSF and other thermal desalination processes.