This paper presents a study of electrokinetic transport in a nano-fluidic chip that allows for the selection and pre-concentration of molecular mixtures by a high density multi-wall carbon nanotubes array (MCNTs) in nano-channels. Parylene (poly(p-xylylene)) was deposited on MWCNTs walls as a dielectric material, the surface charge characters and density could adjusted when an induced polarizes filed was applied. The MCNTs array was used as an induced-surface charge filter to attract the charged molecules on the wall surface by van der Waals and electrostatic force. The surface charge of MCNTs is inversely proportional to the channel wall thickness and proportional to the dielectric constant of Parylene thin layer as well as the applied external electric-field. The competition between electroosmotic dragging force and nonlinear electrophoretic forces induced by polarization effect is suggested responsible for the setup of two preconcentration regimes at both cathodic and anodic sides of the nanochannel. A 105-6 folds high concentration capability of FITC-labelied IgG has been achieved in 15 min in this device which is not easily carried out by standard MEMS process. The fabrication of this device with direct growth of MWCNTs inside nanochannel is first reported to apply to electro-preconcentration.