A quasi-one-dimensional Poisson–Nernst–Planck system for ionic flow through a membrane channel is studied. Nonzero but small permanent charge, the major structural quantity of an ion channel, is included in the model. The system includes three ion species, two cations with the same valences and one anion, which provides more correlations/interactions between ions compared to the case included only two oppositely charged particles. The cross-section area of the channel is included in the system, which provides certain information of the geometry of the three-dimensional channel. This is crucial for our analysis. Under the framework of geometric singular perturbation theory, more importantly, the specific structure of the model, the existence and local uniqueness of solutions to the system for small permanent charges is established. Furthermore, treating the permanent charge as a small parameter, through regular perturbation analysis, we are able to derive approximations of the individual fluxes explicitly, and this allows us to examine the small permanent charge effects on ionic flows in detail. Of particular interest is the competition between two cations, which is related to the selectivity phenomena of ion channels. Critical potentials are identified and their roles in characterizing ionic flow properties are studied. Some critical potentials can be estimated experimentally, and this provides an efficient way to adjust/control boundary conditions (electric potential and concentrations) to observe distinct qualitative properties of ionic flows. Mathematical analysis further indicates that to optimize the effect of permanent charges, a short and narrow filter, within which the permanent charge is confined, is expected, which is consistent with the typical structure of an ion channel.