The FeCrAl alloy has been considered a potential candidate material for bipolar plates (BPs) in fuel cells, emphasizing the improvement of corrosion resistance through surface modification. This study involves a selective etching process that facilitates the preferential dissolution of iron ions to establish a high-chromium surface, enhancing both corrosion resistance and hydrophobic properties. This crucial etching process alters the surface roughness and enhances the surface energy. The transformed rough surface due to surface polishing and etching changes from hydrophilic to hydrophobic, which facilitates corrosion management and moisture control based on the Cassie-Baxter model. The modified micro/nanostructure of the FeCrAl alloy surface and the reconstituted protective film exhibit excellent corrosion inhibition and long-term stability. The study elucidates how the correlation between surface free energy (SFE) and the formation of hydrophobic and rough surfaces acts as a mechanism for enhancing the corrosion resistance of FeCrAl surfaces. Utilizing the Van Oss-Chaudhury-Good (Van Oss) method based on the Lewis acid/base theory further clarifies this corrosion inhibition process, proposing a novel approach that offers significant advantages over traditional methods. Furthermore, this method offers economic and efficient benefits compared with traditional coating methods, providing a promising avenue for reliable corrosion protection in fuel cell applications.