A molecular dynamics (MD) model of the fluidic electrokinetic transport in a nano-scale channel with two bulk sinks was presented, and the process of ion transport in the nanochannel was simulated in this paper. The model consists of two water sinks at the two ends and a pump in the middle, which is different from a single pump model in previous MD simulations. Simulation results show that the charged surfaces of the nanochannel result in the depletion of co-ions and the enrichment of counterions in the nanochannel. A stable current is induced because of the motion of ions when an external electric field is applied across the nanochannel, and the current in the pump region is mainly induced by the motion of counterions. In addition, the ion number in the pump region rapidly decreases as the external electric field is applied. In the equilibrated system, the electrically neutral character in the pump region is destroyed and this region displays a certain electrical character, which depends on the surface charge. The ion distribution is greatly different from the results predicted by the continuum theory, e.g. a smaller peak value of Na+ concentration appears near the wall. The transport efficiency of counterions (co-ions) can be effectively increased (decreased) by increasing the surface charge density. The simulation results demonstrate that the ion distribution in the electric double layer (EDL) of a nanochannel cannot be exactly described by the classical Gouy-Chapman-Stern (GCS) theory model. The mechanism of some special experimental phenomena in a nanochannel and the effect of the surface charge density on the ion-transport efficiency were also explored to provide some theoretical insights for the design and application of nano-scale fluidic pumps. A molecular dynamics (MD) model of the fluidic electrokinetic transport in a nano-scale channel with two bulk sinks was presented, and the process of ion transport in the nanochannel was simulated in this paper. The model consists of two water sinks at the two ends and a pump in the middle, which is different from a single pump model in previous MD simulations. Simulation results show that the charged surfaces of the nanochannel result in the depletion of co-ions and the enrichment of counterions in the nanochannel. A stable current is induced because of the motion of ions when an external electric field is applied across the nanochannel, and the current in the pump region is predominant by the motion of counterions. external electric field is applied. In the equilibrated system, the electrically neutral character in the pump region is destroyed and this region displays a certain electrical character, which depe nds on the surface charge. The ion distribution is greatly different from the results predicted by the continuum theory, eg, smaller peak value of Na + concentration appears near the wall. The simulation results demonstrate that the ion distribution in the electric double layer (EDL) of a nanochannel can not be exactly described by the classical Gouy-Chapman-Stern (GCS) theory model. The mechanism of some special experimental phenomena in a nanochannel and the effect of the surface charge density on the ion-transport efficiency were also explored to provide some theoretical insights for the design and application of nano-scale fluidic pumps.