A theory for calculating the electrostatic interaction between protein molecules and the wall of a liquid-filled micropore is established in terms of solving the Laplace and the linear Poisson-Boltzmann equations. The surface charge of protein molecules is measured by the electrophoresis velocity, while the charge of the pore wall is obtained by the ionic Donnan equilibrium. The theory is then used to study the influence of solute-pore electrostatic interaction on the concentration partition of protein solution in a micropore under different solution properties. Experimental verification is performed by detecting the hindered diffusion of bovine serum albumin in the track-etched polycarbonate membranes. A good consistence between the theoretical and experimental data is being achieved.