In the present study, we developed a numerical method to investigate the electrokinetic phenomena in nanochannel. The numerical method calculated electric field and ionic distribution in nanochannel including the electric double layer by numerically solving three dimensional Poisson-Nemst-Planck equation. The accuracy was evaluated from the view point of charge neutrality and the electrokinetic potential at the boundary wall. Using the numerical method, we analyzed the electric field and ionic distribution of potassium ion and chlorine ion in the 100nm rectangular nanochannel at various ionic concentrations. The numerical result showed that the electrokinetic potential agreed well with that from the Graham equation at higher concentration c>1.0mol/m^3, but deviated at lower concentrations c<1.0mol/m^3. This electrokinetic phenomenon in the nanochannel was considered to be induced due to the overlapped electric double layer.