To address the escalating demand for anti-corrosive and anti-fouling solutions in marine environments, the development of superhydrophobic bilayer coating based on nanocomposite polymers applied to metal substrates is crucial. However, achieving concurrent anti-corrosive and anti-fouling functionalities remains a formidable challenge. In this study, a nanocomposite polymer coating was created through the star crosslinking of polyhedral oligomeric silsesquioxane (POSS) and fluorinated polyimide (FPI) prepolymer. Subsequently, a double-layer coating featuring a superhydrophobic layer was fashioned using the aforementioned coating as the base layer. Following a 50-day salt spray test, both the FPI/POSS-4 coating and the double-layer superhydrophobic FPI/POSS@POA/F-SiO2 coating demonstrated exemplary corrosion resistance. The impedance modulus (|Z| 0.01 Hz) of FPI/POSS-4 and FPI/POSS@POA/F-SiO2 was 3.17 × 109 and 7.04 × 1010 Ω⋅cm2, respectively, surpassing that of pure FPI coating by approximately two to three orders of magnitude. The enhanced performance for the FPI/POSS-4 single-layer coating resulted from the POSS star crosslinking, which bolstered coating compactness, thereby creating a physical barrier akin to the “labyrinth effect.” This hindered corrosive media penetration, thereby extending the penetration path. Conversely, the latter double-layer coating relied on the exceptional shielding provided by the underlying nanocomposite polymer coating and the inhibitory effects of the superhydrophobic coating against corrosive media. Notably, the fabricated superhydrophobic coating exhibited robust mechanical durability, retaining its superhydrophobicity even after 100 cycles of sandpaper friction and 80 cycles of tape peeling. In addition, the superhydrophobic coating demonstrated self-cleaning and anti-fouling properties. This study offers a fresh perspective on the preparation of double-layer superhydrophobic coatings with outstanding anti-corrosive and anti-fouling attributes, showcasing their potential and prospective practical applications.