Nano-scale confinements within mesoporous systems develop overlapping electric double layers (EDL) such that the existing theoretical models cannot predict the electric potential distributions and resulting surface charges. In addition, ionic conditions undergo local variation through connections between the pore voids and pore throats. For the first time in literature, we studied the charging behavior of mesoporous silica in terms of the pore to throat size ratio (Rpt) to characterize the pore connectivity effects, in addition to porosity (є) and pore size (H). Both local and average surface charge densities inside mesoporous silica were examined by varying these parameters systematically. Results showed that the magnitude of surface charge density decreased with increasing EDL overlap and decreasing connectivity effects. We formulized this behavior and developed an extended model to predict mesoporous silica’s internal charge as a function of porosity, pore size, and pore to throat size ratio.