Inspired by nature, functionalized nanopores have become an important platform in the field of sensing. In this article, we constructed a mathematical model for the gate-controlled manipulation of nanoparticle motion inside pH-responsive polyelectrolyte-modified nanopores and theoretically studied the synergistic control of gate electrode and polyelectrolyte brush layer on nanoparticle motion. By efficiently modifying the charge density and polarity of the polyelectrolyte brush layer located within the nanopore, the gate electrode is capable of actively regulating the velocity of nanoparticle transport through the nanopore. At a solution pH of 5, the higher the gate potential, the faster the nanoparticle transport through the nanopore, which is significantly different from the solution pH of 6. When the gate potential is negative, the degree of ion current blockage increases with increasing gate potential. These results establish a theoretical foundation for the development of novel functionalized nanopores that can be utilized in the field of nanopore sensing.