The electrokinetic conductivity of micro-/nanofluidic systems, which strongly depends on the local solution properties (e.g., pH and ionic strength), has wide applications in nanosystems to control the system performance and ion rectification. Accurate and active manipulation of this parameter is proven to be very challenging since, in nanoscale, the ion transport is particularly dominated by the acquired surface charge on the solid–liquid interfaces. In this study, we propose an approach to manipulate the nanochannel electrokinetic conductivity by changing the pH value of the solution at the inlet in order to impose asymmetrical conditions inside nanochannel. The variable surface charge of walls is determined by considering the chemical adsorption on the solid–liquid interface and the electrical double layer interaction. The presented numerical model, which couples Poisson–Nernst–Planck and Navier–Stokes equations, can fully consider the electro-chemo-mechanical transport phenomena and predict the electrokinetic conductivity of nanofluidic channels with good accuracy. Modeling results show that the electrokinetic conductivity of the nanofluidic systems can be regulated by varying the solution pH at the inlet. It is revealed that the stronger electric double layers interaction can enhance the sensitivity of the nanochannel electrokinetic conductance to the inlet pH. This unique behavior of the nanochannel electrokinetic conductivity could broaden potential applications in biomedical, energy, and environmental systems using nanofluidic devices.