Fouling and biofouling remain significant challenges in seawater desalination plants. One practical approach to address these issues is to develop anti-biofouling membranes. Therefore, novel hybrid zinc phthalocyanine/polyvinylidene fluoride-co-hexafluoropropylene (Zn(4-PPOx)4Pc/PVDF-HFP) membranes were prepared by electrospinning to evaluate their properties against biofouling. The hybrid nanofiber membrane was characterized by atomic force microscopy (AFM), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, and contact angle measurements. The theoretical calculations of PVDF-HFP, Zn(4-PPOx)4Pc), and Zn(4-PPOx)4Pc/PVDF-HFP nanofibers were performed using a hybrid functional RB3LYP and the 6-31 G (d,p) basis set, employing Gaussian 09. DFT calculations illustrated that the calculated physical and electronic parameters ensured the feasibility of the interaction of PVDF-HFP with Zn(4-PPOx)4Pc via a halogen–hydrogen bond, resulting in a highly stable and remarkably reactive structure. Moreover, molecular electrostatic potential (MEP) maps were drawn to identify the reactive regions of the Zn(4-PPOx)4Pc and PVDF-HFP/Zn(4-PPOx)4Pc nanofibers. Molecular docking analysis revealed that Zn(4-PPOx)4Pc has highest binding affinity (−8.56 kcal/mol) with protein from S. aureus (1N67) mainly with ten amino acids (ASP405, LYS374, GLU446, ASN406, ALA441, TYR372, LYS371, TYR448, LYS374, and ALA442). These findings highlight the promising potential of Zn(4-PPOx) 4Pc/PVDF-HFP nanocomposite membranes in improving the efficiency of water desalination by reducing biofouling and providing antibacterial properties.