This research explores ion transport behavior and functionality in a hybrid nanochannel that consists of two conical and cylindrical parts. The numerical investigation focuses on analyzing the length of each part in the nanochannel. The nanochannels are hybrid cavities embedded in a membrane, where the size of the conical part varies as equal to, larger than, or smaller than the cylindrical part. The nanochannel is coated with a polyelectrolyte layer that exhibits a dense charge density distribution. The charge density of the soft layer is described using the soft step distribution function. We study the electroosmotic flow, ionic current, rectification, and selectivity of the nanochannel versus bulk electrolyte concentration, the charge density of the polyelectrolyte layer, and decay length, while considering the effect of ionic partitioning. The steady-state Poisson–Nernst–Planck and Navier–Stokes equations are solved using the finite element method. The findings reveal that the nanochannel with a more extensive conical section demonstrates increased rectification, with the rectification factor rising from 1.4 to 2 at a bulk concentration of 100 mM. Additionally, the nanochannel with a longer cylindrical part exhibits improved selectivity under negative voltage conditions, while positive voltage introduces a different situation. The nanochannel with equal cylindrical and conical parts significantly affects conductivity by modifying the charge density in the soft layer, resulting in a 3.125-fold increase in conductivity under positive voltage when the charge density in the polyelectrolyte layer is raised from 25 to 100 mol m⁻³. This research focuses on creating intelligent nanochannels by controlling mass concentration, charge density, and collapse length, improving system performance, and optimizing properties. It also offers valuable insights into ion transport mechanisms in nanochannel systems, advancing our understanding in this field.