Abstract: Molecular simulations were performed to simulate the transport process of biomolecules in parallel-plate nanofluidic channels based on GROMACS program package. Models were built with a series of simplifications and assumptions and simulated the process in the 3.1 nm high channel. Then the simulation results were discussed, such as the RMSD (root mean square deviations), density distribution of water molecules, and concentration distribution of the ions. The following conclusions were drawn: near the channel wall, water molecules delaminate and form compact layers with a density high up to 2500 kg/m³ while the distribution is smooth in the middle area. The protein molecules pass through the channel along the electric field direction accompanying with rotations and translations due to the function of ions and electric field. The main reason for the charge inversion phenomenon is the electrostatic effect of the channel wall on the ions after comparing the ion distributions under charged and uncharged surfaces.