The separation efficiency of pressure-driven filtration membranes is primarily dictated by the membrane pore size. Membranes with larger pores typically demonstrate high flux but low or zero rejection when it comes to separating small molecules. In protein separation, ultrafiltration (UF) membranes with pore sizes smaller than the molecular dimensions of target proteins are commonly used for size rejection. Taking inspiration from the separation mechanism of nanofiltration (NF) membranes, we hypothesize that introducing charged groups into membranes of appropriate pore sizes could significantly enhance the electrical interaction between membrane charges and protein charges. This enhancement, occurring at the nanoscale distance when protein molecules approach or pass through charged nanoscale membrane channels, may enable the rejection of proteins substantially smaller than the pore size. Using membranes with relatively large pore sizes could lead to an increase in flux. To test this hypothesis, we conducted experiments involving the modification of polyvinylidene fluoride (PVDF) membranes with suitable pore sizes, using polyamidoamine (PAMAM) dendrimers to introduce negative charges to the membranes. The performance of the PVDF membranes and the modified membranes were investigated in the separation of whey proteins. To evaluate the contribution of steric and electrical hindrance to the solute separation, filtration experiments were performed using polyethylene oxide (PEO) and polyacrylic acid (PAA). The membranes were characterized using techniques such as attenuated total reflectance-Fourier transform infrared (ATR-FTIR), X-ray photoelectron spectroscopy (XPS), and scanning electron microscopy (SEM). The results indicate that the modification enhances the rejection efficiency of whey proteins. The whey protein rejection and permeate flux for PVDF membranes were 58.9% and 15.3 LMH, respectively. Following alkaline treatment or PAMAM-G3.5 dendrimer modification, the whey protein rejection increased to 97.3% and 98.8%, respectively. However, alkaline treatment and PAMAM-G3.5 dendrimer modification resulted in a reduction of permeate flux to 5.6 LMH and 2.3 LMH, respectively. This suggests that increasing membrane charge effectively enhances the separation ability of filtration membranes in charged macromolecule separation.