Polyvinylidene fluoride (PVDF) membranes, widely used for their stability, face limitations due to the hardly adjustable pore size in nanoscale and inherent hydrophobicity. To address this, we proposed a co-deposition method incorporating dopamine (DA), polyethyleneimine (PEI), and silicon dioxide (SiO2) nanoparticles with glutaraldehyde cross-linking for precise regulation of pore size and hydrophilicity in PVDF hollow fiber membranes. Notably, the pore diameter reduced from 119.0 ± 3.55 nm to 18.4 ± 0.36 nm, while the contact angle decreased from 107.7° to 40.9°. This simultaneous regulation led to a high-performance PDA/PEI/SiO2-PVDF hydrophilic ultrafiltration membrane with a rejection rate exceeding 99% for 20 nm nanoparticles in a long-term simulated separation experiment while achieving a significant protein permeability of 97% in BSA permeation experiments. Additionally, the membrane demonstrated exceptional long-term stability, offering a novel approach for tuning the performance of ultrafiltration/microfiltration membranes.