Polyvinylidene fluoride (PVDF) membranes represent a potential technology for the in-depth treatment of organic dye-containing wastewater. Nevertheless, the intractable membrane fouling and the limited versatility have significantly constrained its applications. Herein, through the nonsolvent-induced phase inversion method, we have successfully fabricated the PDA@MgO/PVDF and PDA@ZnO/PVDF membranes, which are modified by the synergistic action of MgO or ZnO nanoparticles with polydopamine (PDA), respectively. Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), as well as the analyses of pore structure, contact angle, and surface free energy, were utilized to characterize the hybrid membranes. The results demonstrate that the modification of PDA@MgO and PDA@ZnO can enhance the hydrophilicity, pure flux, dye rejection, and pollution resistance of PVDF membranes. The enhanced hydrophilicity of the modified membranes results from the increase in surface free energy and its polar component term. Comparatively, the PDA@ZnO/PVDF membrane exhibits a smaller contact angle (69°) and a higher pure water flux (378.63 L/m2·h·bar), whereas the PDA@MgO/PVDF membrane possesses greater mechanical strength and better antifouling performance. The PDA@MgO/PVDF membrane can achieve a rejection rate of 94.6% for disperse deep blue 79, and the flux recovery rate can reach approximately 82%. This research offers novel insights into the application of PVDF membranes for the treatment of organic dye-containing wastewater.